De novo assembly of Dekkera bruxellensis: a multi technology approach using short and long-read sequencing and optical mapping

Single-molecule analysis reveals widespread structural variation in multiple myeloma

(2015) Aditya Gupta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Whole-genome mapping for high-resolution genotyping of Pseudomonas aeruginosa

(2014) S.A. Boers et al.   JOURNAL OF MICROBIOLOGICAL METHODS

A High-Definition View of Functional Genetic Variation from Natural Yeast Genomes

(2014) Anders Bergström et al.   MOLECULAR BIOLOGY AND EVOLUTION

Resolving the complexity of the human genome using single-molecule sequencing

(2014) Mark J. P. Chaisson et al.   NATURE

Large Chromosomal Rearrangements during a Long-Term Evolution Experiment with Escherichia coli

(2014) C. Raeside et al.   mBio

High-quality genome (re)assembly using chromosomal contact data

(2014) Hervé Marie-Nelly et al.   Nature Communications

ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies

(2013) Scott C. Clark et al.   BIOINFORMATICS

GAM-NGS: genomic assemblies merger for next generation sequencing

(2013) Riccardo Vicedomini et al.   BMC BIOINFORMATICS

Whole-Genome Mapping: a New Paradigm in Strain-Typing Technology

(2013) J. M. Miller   JOURNAL OF CLINICAL MICROBIOLOGY

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

A single-molecule long-read survey of the human transcriptome

(2013) Donald Sharon et al.   NATURE BIOTECHNOLOGY

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

CGAL: computing genome assembly likelihoods

(2013) Atif Rahman et al.   GENOME BIOLOGY

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

(2013) Keith R Bradnam et al.   GigaScience

Intraspecific variations of Dekkera/Brettanomyces bruxellensis genome studied by capillary electrophoresis separation of the intron splice site profiles

(2012) Ileana Vigentini et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

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

(2012) Yang Dong et al.   NATURE BIOTECHNOLOGY

A hybrid approach for the automated finishing of bacterial genomes

(2012) Ali Bashir et al.   NATURE BIOTECHNOLOGY

Feature-by-Feature – Evaluating De Novo Sequence Assembly

(2012) Francesco Vezzi et al.   PLoS One

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

(2012) Ruibang Luo et al.   GigaScience

Assemblathon 1: A competitive assessment of de novo short read assembly methods

(2011) D. Earl et al.   GENOME RESEARCH

GAGE: A critical evaluation of genome assemblies and assembly algorithms

(2011) S. L. Salzberg et al.   GENOME RESEARCH

Comparative Functional Genomics of the Fission Yeasts

(2011) N. Rhind et al.   SCIENCE

Genome Evolution in the Eremothecium Clade of the Saccharomyces Complex Revealed by Comparative Genomics

(2011) Jürgen Wendland et al.   G3-Genes Genomes Genetics

Yeast evolutionary genomics

(2010) Bernard Dujon   NATURE REVIEWS GENETICS

High-resolution human genome structure by single-molecule analysis

(2010) B. Teague et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Two genome sequences of the same bacterial strain, Gluconacetobacter diazotrophicus PAl 5, suggest a new standard in genome sequence submission

(2010) Adriana Giongo et al.   Standards in Genomic Sciences

Complex Nature of the Genome in a Wine Spoilage Yeast,Dekkera bruxellensis

(2009) Linda Hellborg et al.   EUKARYOTIC CELL

Comparative genomics of protoploid Saccharomycetaceae

(2009) et al.   GENOME RESEARCH

Comparative genomics of the fungal pathogens Candida dubliniensis and Candida albicans

(2009) A. P. Jackson et al.   GENOME RESEARCH

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae

(2009) Joseph Schacherer et al.   NATURE

Population genomics of domestic and wild yeasts

(2009) Gianni Liti et al.   NATURE

Genome Project Standards in a New Era of Sequencing

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

Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse

(2009) Deanna M. Church et al.   PLOS BIOLOGY

A Single Molecule Scaffold for the Maize Genome

(2009) Shiguo Zhou et al.   PLoS Genetics

The Genome of Nectria haematococca: Contribution of Supernumerary Chromosomes to Gene Expansion

(2009) Jeffrey J. Coleman et al.   PLoS Genetics

Aggressive assembly of pyrosequencing reads with mates

(2008) Jason R. Miller et al.   BIOINFORMATICS

Mapping and sequencing of structural variation from eight human genomes

(2008) Jeffrey M. Kidd et al.   NATURE

The minimum information about a genome sequence (MIGS) specification

(2008) Dawn Field et al.   NATURE BIOTECHNOLOGY