(Q28686251)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23716638%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

title

Computational analysis of bacterial RNA-Seq data (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23716638%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

1 reference

1 reference

1 reference

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23716638%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

Ryan S McClure

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23716638%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

author name string

Divya Balasubramanian

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23716638%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

Yan Sun

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23716638%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

Maksym Bobrovskyy

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23716638%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

Caroline A Genco

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23716638%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

Carin K Vanderpool

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23716638%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

Brian Tjaden

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23716638%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

language of work or name

English

0 references

publication date

28 May 2013

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23716638%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

published in

Nucleic Acids Research

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23716638%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

volume

41

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23716638%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

issue

14

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23716638%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

page(s)

e140

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23716638%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 3.0 Unported

2 March 2020

copyright license

start time

5 October 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

Bayes' theorem

1 reference

18 June 2022

https://europepmc.org/article/PMC/3737546

inferred from PubMed Central ID database lookup

cites work

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Fast gapped-read alignment with Bowtie 2

17 March 2017

1 reference

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The group A Streptococcus small regulatory RNA FasX enhances streptokinase activity by increasing the stability of the ska mRNA transcript

17 March 2017

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Rfam: Wikipedia, clans and the "decimal" release

17 March 2017

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RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)

17 March 2017

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Differential expression analysis for sequence count data

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

17 March 2017

1 reference

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The primary transcriptome of the major human pathogen Helicobacter pylori

17 March 2017

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SOAP2: an improved ultrafast tool for short read alignment

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

Fast and accurate short read alignment with Burrows-Wheeler transform

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

RNA-Seq: a revolutionary tool for transcriptomics

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

Mapping and quantifying mammalian transcriptomes by RNA-Seq

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

Microbial community gene expression in ocean surface waters

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

Involvement of a novel transcriptional activator and small RNA in post-transcriptional regulation of the glucose phosphoenolpyruvate phosphotransferase system

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

Novel small RNA-encoding genes in the intergenic regions of Escherichia coli

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

Expression of the glucose transporter gene, ptsG, is regulated at the mRNA degradation step in response to glycolytic flux in Escherichia coli

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

Base-calling of automated sequencer traces using phred. II. Error probabilities

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

Base-calling of automated sequencer traces using phred. I. Accuracy assessment

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

Identification of common molecular subsequences

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

Integrative genomics viewer

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

Dual RNA-seq of pathogen and host

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

GC-content normalization for RNA-Seq data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

Genome-wide antisense transcription drives mRNA processing in bacteria

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

Assessing computational tools for the discovery of small RNA genes in bacteria

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

Genome-wide detection of novel regulatory RNAs in E. coli

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

Studying bacterial transcriptomes using RNA-seq

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

A survey of sequence alignment algorithms for next-generation sequencing

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

A single-base resolution map of an archaeal transcriptome

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

Computation for ChIP-seq and RNA-seq studies

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

Characterization of homologs of the small RNA SgrS reveals diversity in function

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

Structure and complexity of a bacterial transcriptome.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

Statistical inferences for isoform expression in RNA-Seq

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

DOOR: a database for prokaryotic operons

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

The relative value of operon predictions.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

Small-sample estimation of negative binomial dispersion, with applications to SAGE data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

Operon prediction using both genome-specific and general genomic information

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

Co-expression pattern from DNA microarray experiments as a tool for operon prediction

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

Physical map of the chromosome of Neisseria gonorrhoeae FA1090 with locations of genetic markers, including opa and pil genes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3737546

Immunological basis of serum resistance of Neisseria gonorrhoeae.

3 June 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKT444

Operon prediction without a training set.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKT444

A Bayesian network approach to operon prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKT444

Generating samples under a Wright-Fisher neutral model of genetic variation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKT444

Transcriptome Complexity in a Genome-Reduced Bacterium

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKT444

Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity

21 January 2018

1 reference

12 December 2020

Identifying operons and untranslated regions of transcripts using Escherichia coli RNA expression analysis

1 reference

12 December 2020

Evidence for two functional gal promoters in intact Escherichia coli cells

1 reference

12 December 2020

Relationship between gene expression and GC-content in mammals: statistical significance and biological relevance

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKT444

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23716638%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

1 reference

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23716638%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

2 references