Improvement of the banana “Musa acuminata” reference sequence using NGS data and semi-automated bioinformatics methods

Misassembly detection using paired-end sequence reads and optical mapping data

(2015) Martin D. Muggli et al.   BIOINFORMATICS

Genome-wide survey of the seagrass Zostera muelleri suggests modification of the ethylene signalling network

(2015) Agnieszka A. Golicz et al.   JOURNAL OF EXPERIMENTAL BOTANY

Assembly and diploid architecture of an individual human genome via single-molecule technologies

(2015) Matthew Pendleton et al.   NATURE METHODS

SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information

(2014) Marten Boetzer et al.   BMC BIOINFORMATICS

Expansion of banana (Musa acuminata) gene families involved in ethylene biosynthesis and signalling after lineage-specific whole-genome duplications

(2014) Cyril Jourda et al.   NEW PHYTOLOGIST

Tangled up in two: a burst of genome duplications at the end of the Cretaceous and the consequences for plant evolution

(2014) Kevin Vanneste et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Evolutionary divergence of β-expansin structure and function in grasses parallels emergence of distinctive primary cell wall traits

(2014) Javier Sampedro et al.   PLANT JOURNAL

Genomic analysis of NAC transcription factors in banana (Musa acuminata) and definition of NAC orthologous groups for monocots and dicots

(2014) Albero Cenci et al.   PLANT MOLECULAR BIOLOGY

Genetic anchoring of whole-genome shotgun assemblies

(2014) Martin Mascher et al.   Frontiers in Genetics

Beyond sequencing: optical mapping of DNA in the age of nanotechnology and nanoscopy

(2013) Michal Levy-Sakin et al.   CURRENT OPINION IN BIOTECHNOLOGY

Plant genome sequencing — applications for crop improvement

(2013) Marie E Bolger et al.   CURRENT OPINION IN BIOTECHNOLOGY

Two Evolutionarily Distinct Classes of Paleopolyploidy

(2013) Olivier Garsmeur et al.   MOLECULAR BIOLOGY AND EVOLUTION

P-MITE: a database for plant miniature inverted-repeat transposable elements

(2013) Jiongjiong Chen et al.   NUCLEIC ACIDS RESEARCH

Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)

(2013) Martin Mascher et al.   PLANT JOURNAL

Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants

(2013) R. De Smet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Banana Genome Hub

(2013) Gaëtan Droc et al.   Database-The Journal of Biological Databases and Curation

The First 50 Plant Genomes

(2013) Todd P. Michael et al.   Plant Genome

GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies

(2012) A. A. Gritsenko et al.   BIOINFORMATICS

SCARPA: scaffolding reads with practical algorithms

(2012) N. Donmez et al.   BIOINFORMATICS

Paired-end sequencing of Fosmid libraries by Illumina

(2012) L. J. S. Williams et al.   GENOME RESEARCH

The banana (Musa acuminata) genome and the evolution of monocotyledonous plants

(2012) Angélique D’Hont et al.   NATURE

Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)

(2012) Yang Dong et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs

(2012) Martin T Swain et al.   Nature Protocols

Current challenges in de novo plant genome sequencing and assembly

(2012) Michael C Schatz et al.   GENOME BIOLOGY

Toward almost closed genomes with GapFiller

(2012) Marten Boetzer et al.   GENOME BIOLOGY

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Fast scaffolding with small independent mixed integer programs

(2011) L. Salmela et al.   BIOINFORMATICS

Optical mapping of DNA: Single-molecule-based methods for mapping genomes

(2011) Robert K. Neely et al.   BIOPOLYMERS

Multipoint maximum likelihood mapping in a full-sib family of an outbreeding species

(2011) J. W. VAN OOIJEN   Genetics Research

Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences

(2011) Song Gao et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A decade’s perspective on DNA sequencing technology

(2011) Elaine R. Mardis   NATURE

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

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

SOPRA: Scaffolding algorithm for paired reads via statistical optimization

(2010) Adel Dayarian et al.   BMC BIOINFORMATICS

Limitations of next-generation genome sequence assembly

(2010) Can Alkan et al.   NATURE METHODS

Crop genome sequencing: lessons and rationales

(2010) Catherine Feuillet et al.   TRENDS IN PLANT SCIENCE

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Genome Project Standards in a New Era of Sequencing

(2009) P. S. G. Chain et al.   SCIENCE