(Q30872404)

14 November 2017

Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq (English)

1 reference

14 November 2017

Austin G Meyer

9

0 references

Jeffrey E Barrick

1

object named as

Jeffrey E Barrick

1 reference

14 November 2017

Geoffrey Colburn

2

1 reference

14 November 2017

Daniel E Deatherage

3

1 reference

14 November 2017

Charles C Traverse

4

1 reference

14 November 2017

Matthew D Strand

5

1 reference

14 November 2017

Jordan J Borges

6

1 reference

14 November 2017

David B Knoester

7

1 reference

14 November 2017

Aaron Reba

8

1 reference

14 November 2017

language of work or name

English

0 references

publication date

29 November 2014

1 reference

14 November 2017

1 reference

14 November 2017

15

1 reference

14 November 2017

1039

1 reference

describes a project that uses

14 November 2017

MUMmer

object named as

MUMmer

1 reference

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

exact match

https://scigraph.springernature.com/pub.10.1186/1471-2164-15-1039

0 references

cites work

Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300727

Bacteriophages use an expanded genetic code on evolutionary paths to higher fitness

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300727

Genome dynamics during experimental evolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300727

Genomically recoded organisms expand biological functions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300727

Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300727

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300727

Evolutionary remodeling of global regulatory networks during long-term bacterial adaptation to human hosts

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300727

Parallel evolutionary dynamics of adaptive diversification in Escherichia coli

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300727

Tangled bank of experimentally evolved Burkholderia biofilms reflects selection during chronic infections

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300727

Genomic analysis of a key innovation in an experimental Escherichia coli population

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300727

Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300727

The multiplicity of divergence mechanisms in a single evolving population

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300727

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300727

Using Tablet for visual exploration of second-generation sequencing data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300727

Fast gapped-read alignment with Bowtie 2

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300727

Summarizing and correcting the GC content bias in high-throughput sequencing

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300727

Clonal evolution in cancer

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300727

Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300727

TopHat-Fusion: an algorithm for discovery of novel fusion transcripts

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300727

Stock culture heterogeneity rather than new mutational variation complicates short-term cell physiology studies of Escherichia coli K-12 MG1655 in continuous culture.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300727

The variant call format and VCFtools

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300727

FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300727

Evolution combined with genomic study elucidates genetic bases of isobutanol tolerance in Escherichia coli

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300727

Identification of fusion genes in breast cancer by paired-end RNA-sequencing

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300727

FusionSeq: a modular framework for finding gene fusions by analyzing Paired-End RNA-Sequencing data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300727

SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300727

Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300727

Use of high throughput sequencing to observe genome dynamics at a single cell level

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300727

Genome evolution and adaptation in a long-term experiment with Escherichia coli

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300727

Genome-wide mutational diversity in an evolving population of Escherichia coli

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300727

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300727

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300727

The Sequence Alignment/Map format and SAMtools

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300727

Circular binary segmentation for the analysis of array-based DNA copy number data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300727

Versatile and open software for comparing large genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300727

Mechanisms causing rapid and parallel losses of ribose catabolism in evolving populations of Escherichia coli B.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300727

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300727

The invertible P-DNA segment in the chromosome of Escherichia coli

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4300727

Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly

21 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2F1471-2164-15-1039

The molecular diversity of adaptive convergence.

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2F1471-2164-15-1039

Genome sequences of Escherichia coli B strains REL606 and BL21(DE3).

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2F1471-2164-15-1039

10.1186/1471-2164-15-1039

21 January 2018

Identifiers

DOI

1 reference

Dimensions Publication ID

14 November 2017

0 references

1 reference

14 November 2017

1 reference