Fine De Novo Sequencing of a Fungal Genome Using only SOLiD Short Read Data: Verification on Aspergillus oryzae RIB40

Parameters for accurate genome alignment

(2012) Martin C Frith et al.   BMC BIOINFORMATICS

Comparative Genome Analysis Between Aspergillus oryzae Strains Reveals Close Relationship Between Sites of Mutation Localization and Regions of Highly Divergent Genes among Aspergillus Species

(2012) M. Umemura et al.   DNA RESEARCH

Advances in Aspergillus secondary metabolite research in the post-genomic era

(2012) James F. Sanchez et al.   NATURAL PRODUCT REPORTS

The Quest for Rare Variants: Pooled Multiplexed Next Generation Sequencing in Plants

(2012) Fabio Marroni et al.   Frontiers in Plant Science

Comparative studies of de novo assembly tools for next-generation sequencing technologies

(2011) Yong Lin et al.   BIOINFORMATICS

First complete genome sequence of infectious laryngotracheitis virus

(2011) Sang-Won Lee et al.   BMC GENOMICS

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

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

(2011) D. Earl et al.   GENOME RESEARCH

Whole-Genome Shotgun Sequencing of the Sulfur-Oxidizing Chemoautotroph Tetrathiobacter kashmirensis

(2011) W. Ghosh et al.   JOURNAL OF BACTERIOLOGY

Aflatoxin non-productivity of Aspergillus oryzae caused by loss of function in the aflJ gene product

(2011) Takuro Kiyota et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

Whole genome sequencing of environmental Vibrio cholerae O1 from 10 nanograms of DNA using short reads

(2011) Paula Juliana Pérez Chaparro et al.   JOURNAL OF MICROBIOLOGICAL METHODS

A biologist's guide to de novo genome assembly using next-generation sequence data: A test with fungal genomes

(2011) Sajeet Haridas et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study

(2011) Louise Teixeira Cerdeira et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Transcriptional regulatory elements in fungal secondary metabolism

(2011) Wenbing Yin et al.   JOURNAL OF MICROBIOLOGY

Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss

(2010) Henk C den Bakker et al.   BMC GENOMICS

Secondary metabolism in fungi: does chromosomal location matter?

(2010) Jonathan M Palmer et al.   CURRENT OPINION IN MICROBIOLOGY

Identification and characterization of genes responsible for biosynthesis of kojic acid, an industrially important compound from Aspergillus oryzae

(2010) Yasunobu Terabayashi et al.   FUNGAL GENETICS AND BIOLOGY

Complete Genome Sequence of Corynebacterium pseudotuberculosis I19, a Strain Isolated from a Cow in Israel with Bovine Mastitis

(2010) A. Silva et al.   JOURNAL OF BACTERIOLOGY

Incorporating sequence quality data into alignment improves DNA read mapping

(2010) Martin C. Frith et al.   NUCLEIC ACIDS RESEARCH

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

Genome Expansion and Gene Loss in Powdery Mildew Fungi Reveal Tradeoffs in Extreme Parasitism

(2010) P. D. Spanu et al.   SCIENCE

De novo Assembly of a 40 Mb Eukaryotic Genome from Short Sequence Reads: Sordaria macrospora, a Model Organism for Fungal Morphogenesis

(2010) Minou Nowrousian et al.   PLoS Genetics

Sequences of complete human cytomegalovirus genomes from infected cell cultures and clinical specimens

(2009) C. Cunningham et al.   JOURNAL OF GENERAL VIROLOGY

Beyond aflatoxin: four distinct expression patterns and functional roles associated withAspergillus flavussecondary metabolism gene clusters

(2009) D. RYAN GEORGIANNA et al.   MOLECULAR PLANT PATHOLOGY

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

SHRiMP: Accurate Mapping of Short Color-space Reads

(2009) Stephen M. Rumble et al.   PLoS Computational Biology

De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data

(2009) Scott DiGuistini et al.   GENOME BIOLOGY

ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads

(2009) Iain MacCallum et al.   GENOME BIOLOGY

De novoassembly of thePseudomonas syringaepv.syringaeB728a genome using Illumina/Solexa short sequence reads

(2008) Rhys A. Farrer et al.   FEMS MICROBIOLOGY LETTERS

Genetic regulation of aflatoxin biosynthesis: From gene to genome

(2008) D. Ryan Georgianna et al.   FUNGAL GENETICS AND BIOLOGY

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

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