(Q35107335)

6 August 2017

title

RNA CoMPASS: a dual approach for pathogen and host transcriptome analysis of RNA-seq datasets (English)

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6 August 2017

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5

Erik K Flemington

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6 August 2017

Guorong Xu

1

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6 August 2017

Michael J Strong

2

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6 August 2017

Michelle R Lacey

3

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6 August 2017

Carl Baribault

4

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6 August 2017

Christopher M Taylor

6

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6 August 2017

language of work or name

English

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publication date

25 February 2014

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6 August 2017

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6 August 2017

volume

9

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6 August 2017

issue

2

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6 August 2017

page(s)

e89445

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Creative Commons Attribution 4.0 International

6 August 2017

copyright license

start time

25 February 2014

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April 2022 Public Data File from Crossref

copyright status

copyrighted

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describes a project that uses

edgeR

object named as

edgeR

1 reference

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

cites work

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Differences in gastric carcinoma microenvironment stratify according to EBV infection intensity: implications for possible immune adjuvant therapy

9 July 2018

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Dual RNA-seq of pathogen and host

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934900

Burkitt lymphoma pathogenesis and therapeutic targets from structural and functional genomics

9 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934900

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

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934900

Identification of new viral genes and transcript isoforms during Epstein-Barr virus reactivation using RNA-Seq

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934900

Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934900

Integrative analysis of environmental sequences using MEGAN4

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934900

The sensitivity of massively parallel sequencing for detecting candidate infectious agents associated with human tissue

9 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934900

PathSeq: software to identify or discover microbes by deep sequencing of human tissue

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934900

Isoform-level microRNA-155 target prediction using RNA-seq

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934900

SAMMate: a GUI tool for processing short read alignments in SAM/BAM format

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934900

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934900

High dose intensity doxorubicin in aggressive non-Hodgkin's lymphoma: a literature-based meta-analysis

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934900

De novo transcriptome assembly with ABySS.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934900

TopHat: discovering splice junctions with RNA-Seq

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934900

c-Myc and Rel/NF-kappaB are the two master transcriptional systems activated in the latency III program of Epstein-Barr virus-immortalized B cells

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934900

Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934900

Topoisomerase levels determine chemotherapy responsein vitroandin vivo

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934900

Clonal integration of a polyomavirus in human Merkel cell carcinoma

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934900

Human transcriptome subtraction by using short sequence tags to search for tumor viruses in conjunctival carcinoma

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934900

c-MYC impairs immunogenicity of human B cells

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934900

Transcriptional regulation and transformation by Myc proteins

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934900

Role of NF-kappa B in cell survival and transcription of latent membrane protein 1-expressing or Epstein-Barr virus latency III-infected cells

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934900

A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934900

Pathogen discovery from human tissue by sequence-based computational subtraction

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934900

Identification of foreign gene sequences by transcript filtering against the human genome

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934900

The transcriptional program of a human B cell line in response to Myc

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934900

The Epstein-Barr virus latent membrane protein-1 (LMP1) mediates activation of NF-kappa B and cell surface phenotype via two effector regions in its carboxy-terminal cytoplasmic domain.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934900

Basic local alignment search tool

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3934900

Molecular diagnosis of Burkitt's lymphoma

9 July 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0089445

A biologic definition of Burkitt's lymphoma from transcriptional and genomic profiling.

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0089445

Prognostic significance of actual dose intensity in diffuse large-cell lymphoma: results of a tree-structured survival analysis

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24586784

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0089445

1 reference

6 August 2017

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6 August 2017

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