(Q30625182)

16 August 2017

Fine de novo sequencing of a fungal genome using only SOLiD short read data: verification on Aspergillus oryzae RIB40. (English)

1 reference

16 August 2017

Aspergillus oryzae

1 reference

Myco Umemura

1

0 references

Masayuki Machida

7

object named as

Masayuki Machida

1 reference

16 August 2017

Yoshinori Koyama

2

1 reference

16 August 2017

Itaru Takeda

3

1 reference

16 August 2017

Hiroko Hagiwara

4

1 reference

16 August 2017

Tsutomu Ikegami

5

1 reference

16 August 2017

Hideaki Koike

6

1 reference

16 August 2017

language of work or name

English

0 references

publication date

7 May 2013

1 reference

16 August 2017

1 reference

16 August 2017

8

1 reference

16 August 2017

5

1 reference

16 August 2017

e63673

1 reference

Creative Commons Attribution 4.0 International

16 August 2017

start time

7 May 2013

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

MUMmer

object named as

MUMmer

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

Comparative genome analysis between Aspergillus oryzae strains reveals close relationship between sites of mutation localization and regions of highly divergent genes among Aspergillus species

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3646829

The quest for rare variants: pooled multiplexed next generation sequencing in plants

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3646829

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3646829

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3646829

Whole-genome shotgun sequencing of the sulfur-oxidizing chemoautotroph Tetrathiobacter kashmirensis.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3646829

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3646829

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3646829

Transcriptional regulatory elements in fungal secondary metabolism

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3646829

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3646829

First complete genome sequence of infectious laryngotracheitis virus

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3646829

Adaptive seeds tame genomic sequence comparison

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3646829

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3646829

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3646829

Complete genome sequence of Corynebacterium pseudotuberculosis I19, a strain isolated from a cow in Israel with bovine mastitis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3646829

Secondary metabolism in fungi: does chromosomal location matter?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3646829

Beyond aflatoxin: four distinct expression patterns and functional roles associated with Aspergillus flavus secondary metabolism gene clusters

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3646829

De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3646829

Parameters for accurate genome alignment

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3646829

Incorporating sequence quality data into alignment improves DNA read mapping

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3646829

The sequence and de novo assembly of the giant panda genome

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3646829

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3646829

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3646829

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3646829

SHRiMP: accurate mapping of short color-space reads

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3646829

Genetic regulation of aflatoxin biosynthesis: from gene to genome

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3646829

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3646829

Molecular analysis of an inactive aflatoxin biosynthesis gene cluster in Aspergillus oryzae RIB strains

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3646829

Genome sequencing and analysis of Aspergillus oryzae

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3646829

Clustered pathway genes in aflatoxin biosynthesis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3646829

Versatile and open software for comparing large genomes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3646829

Nonribosomal peptides: from genes to products

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3646829

Polyketide biosynthesis: a millennium review

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3646829

The parallel and convergent universes of polyketide synthases and nonribosomal peptide synthetases

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3646829

Homologs of aflatoxin biosynthesis genes and sequence of aflR in Aspergillus oryzae and Aspergillus sojae.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3646829

Combined use of sequence similarity and codon bias for coding region identification

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3646829

Twenty-five coregulated transcripts define a sterigmatocystin gene cluster in Aspergillus nidulans

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3646829

Basic local alignment search tool

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3646829

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

20 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0063673

4-[2-(2-amino-2-oxoethyl)-2,7-dihydroxy-4-oxochroman-5-yl]-3-hydroxybut-2-enoic acid

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0063673

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0063673

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0063673

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0063673

Directed deletions in the aflatoxin biosynthesis gene homolog cluster of Aspergillus oryzae

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23667655

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23667655

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0063673

1 reference

16 August 2017

0 references

1 reference

16 August 2017

PubMed publication ID

23667655

1 reference