4.7 Review

Resolving host-pathogen interactions by dual RNA-seq

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemical Research Methods

Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline

Yasir Rahmatallah et al.

BRIEFINGS IN BIOINFORMATICS (2016)

Editorial Material Biochemistry & Molecular Biology

The Overlooked Fact: Fundamental Need for Spike-In Control for Virtually All Genome-Wide Analyses

Kaifu Chen et al.

MOLECULAR AND CELLULAR BIOLOGY (2016)

Article Biochemistry & Molecular Biology

KEGG as a reference resource for gene and protein annotation

Minoru Kanehisa et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemistry & Molecular Biology

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

Ron Caspi et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Multidisciplinary Sciences

Dual RNA-seq unveils noncoding RNA functions in host-pathogen interactions

Alexander J. Westermann et al.

NATURE (2016)

Article Biochemical Research Methods

Spliced synthetic genes as internal controls in RNA sequencing experiments

Simon A. Hardwick et al.

NATURE METHODS (2016)

Review Genetics & Heredity

Coming of age: ten years of next-generation sequencing technologies

Sara Goodwin et al.

NATURE REVIEWS GENETICS (2016)

Article Biochemistry & Molecular Biology

RNA-seq of human reference RNA samples using a thermostable group II intron reverse transcriptase

Ryan M. Nottingham et al.

Review Microbiology

How to Predict Molecular Interactions between Species?

Sylvie Schulze et al.

FRONTIERS IN MICROBIOLOGY (2016)

Article Multidisciplinary Sciences

Dual-seq transcriptomics reveals the battle for iron during Pseudomonas aeruginosa acute murine pneumonia

F. Heath Damron et al.

SCIENTIFIC REPORTS (2016)

Review Biotechnology & Applied Microbiology

A survey of best practices for RNA-seq data analysis

Ana Conesa et al.

GENOME BIOLOGY (2016)

Article Biochemical Research Methods

Practical impacts of genomic data cleaning on biological discovery using surrogate variable analysis

Andrew E. Jaffe et al.

BMC BIOINFORMATICS (2015)

Article Biochemistry & Molecular Biology

Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses

Roi Avraham et al.

Letter Biotechnology & Applied Microbiology

Ballgown bridges the gap between transcriptome assembly and expression analysis

Alyssa C. Frazee et al.

NATURE BIOTECHNOLOGY (2015)

Article Biochemical Research Methods

Orchestrating high-throughput genomic analysis with Bioconductor

Wolfgang Huber et al.

NATURE METHODS (2015)

Review Microbiology

A functional perspective on phenotypic heterogeneity in microorganisms

Martin Ackermann

NATURE REVIEWS MICROBIOLOGY (2015)

Article Biochemistry & Molecular Biology

How data analysis affects power, reproducibility and biological insight of RNA-seq studies in complex datasets

Lucia Peixoto et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Multidisciplinary Sciences

Dual Transcriptomic Profiling of Host and Microbiota during Health and Disease in Pediatric Asthma

Marcos Perez-Losada et al.

PLOS ONE (2015)

Article Multidisciplinary Sciences

Robust bioengineered 3D functional human intestinal epithelium

Ying Chen et al.

SCIENTIFIC REPORTS (2015)

Article Biochemical Research Methods

Comparison of software packages for detecting differential expression in RNA-seq studies

Fatemeh Seyednasrollah et al.

BRIEFINGS IN BIOINFORMATICS (2015)

Article Biochemistry & Molecular Biology

Gene Ontology Consortium: going forward

J. A. Blake et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Biochemical Research Methods

RNA-seq differential expression studies: more sequence or more replication?

Yuwen Liu et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

READemption-a tool for the computational analysis of deep-sequencing-based transcriptome data

Konrad U. Foerstner et al.

BIOINFORMATICS (2014)

Article Biotechnology & Applied Microbiology

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

Kelly J. Pittman et al.

BMC GENOMICS (2014)

Review Biochemistry & Molecular Biology

Molecular Mechanisms Underlying Bacterial Persisters

Etienne Maisonneuve et al.

Article Biotechnology & Applied Microbiology

Normalization of RNA-seq data using factor analysis of control genes or samples

Davide Risso et al.

NATURE BIOTECHNOLOGY (2014)

Editorial Material Biochemical Research Methods

Points of Significance Analysis of variance and blocking

Martin Krzywinski et al.

NATURE METHODS (2014)

Review Genetics & Heredity

Sequencing depth and coverage: key considerations in genomic analyses

David Sims et al.

NATURE REVIEWS GENETICS (2014)

Article Biochemical Research Methods

Tissue fixation and the effect of molecular fixatives on downstream staining procedures

William J. Howat et al.

METHODS (2014)

Article Multidisciplinary Sciences

MARIS: Method for Analyzing RNA following Intracellular Sorting

Sinisa Hrvatin et al.

PLOS ONE (2014)

Article Biochemistry & Molecular Biology

Power analysis and sample size estimation for RNA-Seq differential expression

Travers Ching et al.

Article Infectious Diseases

Dual RNA-seq of Parasite and Host Reveals Gene Expression Dynamics during Filarial Worm-Mosquito Interactions

Young-Jun Choi et al.

PLOS NEGLECTED TROPICAL DISEASES (2014)

Article Biotechnology & Applied Microbiology

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

Charity W. Law et al.

GENOME BIOLOGY (2014)

Article Biotechnology & Applied Microbiology

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

Michael I. Love et al.

GENOME BIOLOGY (2014)

Article Biochemical Research Methods

A comparison of methods for differential expression analysis of RNA-seq data

Charlotte Soneson et al.

BMC BIOINFORMATICS (2013)

Article Biochemical Research Methods

A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

Marie-Agnes Dillies et al.

BRIEFINGS IN BIOINFORMATICS (2013)

Review Microbiology

Heterogeneity of intracellular replication of bacterial pathogens

Sophie Helaine et al.

CURRENT OPINION IN MICROBIOLOGY (2013)

Article Infectious Diseases

Viral-bacterial interactions-therapeutic implications

Jane C. Deng

INFLUENZA AND OTHER RESPIRATORY VIRUSES (2013)

Article Medicine, General & Internal

Bacterial Coinfection in Influenza A Grand Rounds Review

Daniel S. Chertow et al.

JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION (2013)

Article Biochemical Research Methods

Systematic evaluation of spliced alignment programs for RNA-seq data

Par G. Engstrom et al.

NATURE METHODS (2013)

Review Cell Biology

Alternative splicing: a pivotal step between eukaryotic transcription and translation

Alberto R. Kornblihtt et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2013)

Article Biochemistry & Molecular Biology

InnateDB: systems biology of innate immunity and beyond-recent updates and continuing curation

Karin Breuer et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Multidisciplinary Sciences

Chlamydia trachomatis Infection Induces Replication of Latent HHV-6

Bhupesh K. Prusty et al.

PLOS ONE (2013)

Article Multidisciplinary Sciences

Simultaneous Transcriptional Profiling of Bacteria and Their Host Cells

Michael S. Humphrys et al.

PLOS ONE (2013)

Article Biotechnology & Applied Microbiology

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

Franck Rapaport et al.

GENOME BIOLOGY (2013)

Article Biotechnology & Applied Microbiology

How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?

Brian J. Haas et al.

BMC GENOMICS (2012)

Article Biochemistry & Molecular Biology

Revisiting Global Gene Expression Analysis

Jakob Loven et al.

Article Biotechnology & Applied Microbiology

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

Daniel Ramskold et al.

NATURE BIOTECHNOLOGY (2012)

Article Biochemical Research Methods

Wisdom of crowds for robust gene network inference

Daniel Marbach et al.

NATURE METHODS (2012)

Article Biochemical Research Methods

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

Cole Trapnell et al.

NATURE PROTOCOLS (2012)

Review Microbiology

Dual RNA-seq of pathogen and host

Alexander J. Westermann et al.

NATURE REVIEWS MICROBIOLOGY (2012)

Editorial Material Biochemistry & Molecular Biology

Non-genetic diversity shapes infectious capacity and host resistance

Mary K. Stewart et al.

TRENDS IN MICROBIOLOGY (2012)

Article Biochemical Research Methods

Molecular signatures database (MSigDB) 3.0

Arthur Liberzon et al.

BIOINFORMATICS (2011)

Article Biochemistry & Molecular Biology

Phenotypic Landscape of a Bacterial Cell

Robert J. Nichols et al.

Article Biochemistry & Molecular Biology

Transcript amplification from single bacterium for transcriptome analysis

Yun Kang et al.

GENOME RESEARCH (2011)

Article Biochemistry & Molecular Biology

Synthetic spike-in standards for RNA-seq experiments

Lichun Jiang et al.

GENOME RESEARCH (2011)

Article Pathology

The Effect of Formaldehyde Fixation on RNA Optimization of Formaldehyde Adduct Removal

David L. Evers et al.

JOURNAL OF MOLECULAR DIAGNOSTICS (2011)

Review Biochemical Research Methods

Computational methods for transcriptome annotation and quantification using RNA-seq

Manuel Garber et al.

NATURE METHODS (2011)

Article Biochemical Research Methods

RNA-Seq gene expression estimation with read mapping uncertainty

Bo Li et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

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

Mark D. Robinson et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

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

James H. Bullard et al.

BMC BIOINFORMATICS (2010)

Review Genetics & Heredity

Tackling the widespread and critical impact of batch effects in high-throughput data

Jeffrey T. Leek et al.

NATURE REVIEWS GENETICS (2010)

Article Biotechnology & Applied Microbiology

Gene ontology analysis for RNA-seq: accounting for selection bias

Matthew D. Young et al.

GENOME BIOLOGY (2010)

Article Biotechnology & Applied Microbiology

A scaling normalization method for differential expression analysis of RNA-seq data

Mark D. Robinson et al.

GENOME BIOLOGY (2010)

Article Biotechnology & Applied Microbiology

Differential expression analysis for sequence count data

Simon Anders et al.

GENOME BIOLOGY (2010)

Article Microbiology

Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat

Andrew L. Goodman et al.

CELL HOST & MICROBE (2009)

Article Biochemical Research Methods

Digital transcriptome profiling using selective hexamer priming for cDNA synthesis

Christopher D. Armour et al.

NATURE METHODS (2009)

Article Biochemical Research Methods

Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures

Steve Hoffmann et al.

PLOS COMPUTATIONAL BIOLOGY (2009)

Article Pathology

Investigating fixative-induced changes in RNA quality and utility by microarray analysis

Melissa L. Cox et al.

EXPERIMENTAL AND MOLECULAR PATHOLOGY (2008)

Article Pathology

Assessment of fixatives, fixation, and tissue processing on morphology and RNA integrity

ML Cox et al.

EXPERIMENTAL AND MOLECULAR PATHOLOGY (2006)

Article Microbiology

RNA recovery and detection of mRNA by RT-PCR from preserved prokaryotic samples

DS Bachoon et al.

FEMS MICROBIOLOGY LETTERS (2001)