(Q30897629)

14 November 2017

Computational prediction of molecular pathogen-host interactions based on dual transcriptome data (English)

1 reference

14 November 2017

0 references

0 references

4

Reinhard Guthke

1 reference

14 November 2017

5

Jörg Linde

1 reference

14 November 2017

Sylvie Schulze

1

1 reference

14 November 2017

Sebastian G Henkel

series ordinal

2

1 reference

14 November 2017

Dominik Driesch

series ordinal

3

1 reference

14 November 2017

6 February 2015

1 reference

Frontiers in Microbiology

14 November 2017

1 reference

14 November 2017

6

1 reference

14 November 2017

65

1 reference

describes a project that uses

14 November 2017

edgeR

object named as

edgeR

1 reference

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

DESeq2

object named as

DESeq

DESeq2

1 reference

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

DESeq2

0 references

cites work

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

Transcriptional specialization of human dendritic cell subsets in response to microbial vaccines

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

FungiFun2: a comprehensive online resource for systematic analysis of gene lists from fungal species

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

Adaptive prediction as a strategy in microbial 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=4319478

HTSeq--a Python framework to work with high-throughput 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=4319478

Dual transcriptional profiling of mice and Toxoplasma gondii during acute and chronic infection

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

A comparative study of techniques for differential expression analysis on RNA-Seq 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=4319478

Human dendritic cells exhibit a pronounced type I IFN signature following Leishmania major infection that is required for IL-12 induction

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

Trimmomatic: a flexible trimmer for Illumina sequence 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=4319478

Regulatory networks controlling nitrogen sensing and uptake in Candida albicans

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

Comparison of RNA-Seq and microarray in transcriptome profiling of activated T cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

Systematic evaluation of spliced alignment programs for RNA-seq 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=4319478

Simultaneous transcriptome analysis of Sorghum and Bipolaris sorghicola by using RNA-seq in combination with de novo transcriptome assembly

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

PHISTO: pathogen-host interaction search tool

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

A comparison of methods for differential expression analysis of RNA-seq 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=4319478

Inference of dynamical gene-regulatory networks based on time-resolved multi-stimuli multi-experiment data applying NetGenerator V2.0.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

The extended TILAR approach: a novel tool for dynamic modeling of the transcription factor network regulating the adaption to in vitro cultivation of murine hepatocytes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

Dual RNA-seq of pathogen and host

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

GeneView: a comprehensive semantic search engine for PubMed

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

An Interspecies Regulatory Network Inferred from Simultaneous RNA-seq of Candida albicans Invading Innate Immune Cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

Genome-Wide Scale-Free Network Inference for Candida albicans

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

Regulatory interactions for iron homeostasis in Aspergillus fumigatus inferred by a Systems Biology approach

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

Whole-transcriptome RNAseq analysis from minute amount of total RNA.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

Dual organism transcriptomics of airway epithelial cells interacting with conidia of Aspergillus fumigatus

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

Immune escape of the human facultative pathogenic yeast Candida albicans: the many faces of the Candida Pra1 protein

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

A computational framework for gene regulatory network inference that combines multiple methods and datasets

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

Regulatory network modelling of iron acquisition by a fungal pathogen in contact with epithelial cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

HPIDB--a unified resource for host-pathogen interactions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

A biphasic innate immune MAPK response discriminates between the yeast and hyphal forms of Candida albicans in epithelial cells.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

Advantages and limitations of current network inference methods

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

An introduction to effective use of enrichment analysis software

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

edgeR: a Bioconductor package for differential expression analysis of digital gene expression 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=4319478

Gene regulatory network inference: data integration in dynamic models-a review

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

The transcriptional landscape of the yeast genome defined by 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=4319478

Constructing and analyzing a large-scale gene-to-gene regulatory network--lasso-constrained inference and biological validation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

Pathogen recognition and innate immunity

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

Inference of gene regulatory networks and compound mode of action from time course gene expression profiles

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

PHI-base: a new database for pathogen host interactions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

Dynamic network reconstruction from gene expression data applied to immune response during bacterial infection

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

Initial sequencing and analysis of the human genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

Host-pathogen interactions: basic concepts of microbial commensalism, colonization, infection, and disease

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4319478

SiTaR: a novel tool for transcription factor binding site prediction

21 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.3389%2FFMICB.2015.00065

Btrim: a fast, lightweight adapter and quality trimming program for next-generation sequencing technologies.

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.3389%2FFMICB.2015.00065

Current trends in modeling host-pathogen interactions

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.3389%2FFMICB.2015.00065

21 January 2018

1 reference

https://pubmed.ncbi.nlm.nih.gov/25705211

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Pathway studio—the analysis and navigation of molecular networks

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25705211

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.3389/FMICB.2015.00065

1 reference

14 November 2017

1 reference

14 November 2017

PubMed publication ID

25705211

1 reference