A computational genomics pipeline for prokaryotic sequencing projects (Q41866812)

13 October 2017

A computational genomics pipeline for prokaryotic sequencing projects (English)

1 reference

13 October 2017

computational genomics

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Sonia Agrawal

3

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Brian H Harcourt

14

object named as

Brian H Harcourt

1 reference

13 October 2017

15

Leonard W Mayer

1 reference

13 October 2017

Andrey O Kislyuk

1

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13 October 2017

Lee S Katz

2

1 reference

13 October 2017

Matthew S Hagen

4

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13 October 2017

Andrew B Conley

5

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13 October 2017

Pushkala Jayaraman

6

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13 October 2017

Viswateja Nelakuditi

7

1 reference

13 October 2017

Jay C Humphrey

8

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13 October 2017

Scott A Sammons

9

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13 October 2017

Dhwani Govil

10

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13 October 2017

Raydel D Mair

11

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13 October 2017

Kathleen M Tatti

12

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13 October 2017

Maria L Tondella

13

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13 October 2017

I King Jordan

16

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13 October 2017

language of work or name

English

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publication date

2 June 2010

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13 October 2017

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13 October 2017

26

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13 October 2017

15

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13 October 2017

1819-1826

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The integrated microbial genomes system: an expanding comparative analysis resource

13 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

Reordering contigs of draft genomes using the Mauve aligner

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

DIYA: a bacterial annotation pipeline for any genomics lab.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

Estimating the size of the bacterial pan-genome

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

Real-time DNA sequencing from single polymerase molecules

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

Accurate whole human genome sequencing using reversible terminator chemistry

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

Aggressive assembly of pyrosequencing reads with mates

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

The Universal Protein Resource (UniProt) 2009

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

Whole-genome comparison of disease and carriage strains provides insights into virulence evolution in Neisseria meningitidis

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

The RAST Server: rapid annotations using subsystems technology

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

InterPro and InterProScan: tools for protein sequence classification and comparison

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

VFDB 2008 release: an enhanced web-based resource for comparative pathogenomics

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

CAMERA: a community resource for metagenomics

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

Minimus: a fast, lightweight genome assembler

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome"

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

Accurate multiplex polony sequencing of an evolved bacterial genome

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

Genome sequencing in microfabricated high-density picolitre reactors

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

VFDB: a reference database for bacterial virulence factors

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

Mauve: multiple alignment of conserved genomic sequence with rearrangements

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

Improved prediction of signal peptides: SignalP 3.0

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

DNA uptake during bacterial transformation

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

Comparative genomics identifies the genetic islands that distinguish Neisseria meningitidis, the agent of cerebrospinal meningitis, from other Neisseria species

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

5 June 2018

Meningococcal disease

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

Evolutionary trends in the genus Bordetella

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

Improved microbial gene identification with GLIMMER

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

Natural genetic exchange between Haemophilus and Neisseria: intergeneric transfer of chromosomal genes between major human pathogens

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence

5 June 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

5 June 2018

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTQ284

Whole-genome random sequencing and assembly of Haemophilus influenzae Rd

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

Frameshift detection in prokaryotic genomic sequences.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

Pyrobayes: an improved base caller for SNP discovery in pyrosequences.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

The influence of mutation, recombination, population history, and selection on patterns of genetic diversity in Neisseria meningitidis

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

Comparative genome assembly.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

Epidemiology, hypermutation, within-host evolution and the virulence of Neisseria meningitidis.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

The influence of recombination on the population structure and evolution of the human pathogen Neisseria meningitidis

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905547

Comparative genomics of Neisseria meningitidis: core genome, islands of horizontal transfer and pathogen-specific genes

18 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTQ284

10.1093/BIOINFORMATICS/BTQ284

21 January 2018

Identifiers

DOI

1 reference

journals/bioinformatics/KislyukKAHCJNHSGMTTHMJ10

13 October 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

13 October 2017

PubMed publication ID

20519285

1 reference