Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro

Estimating RNA-quality using GeneChip microarrays

(2012) Mario Fasold et al.   BMC GENOMICS

A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae

(2012) Intawat Nookaew et al.   NUCLEIC ACIDS RESEARCH

Global Gene Expression and Systems Biology Analysis of Bovine Monocyte-Derived Macrophages in Response to In Vitro Challenge with Mycobacterium bovis

(2012) David A. Magee et al.   PLoS One

Transcriptional Response of Peripheral Blood Mononuclear Cells from Cattle Infected with Mycobacterium bovis

(2012) Federico Carlos Blanco et al.   PLoS One

Can the battle against tuberculosis gain from epigenetic research?

(2012) Maria M. Esterhuyse et al.   TRENDS IN MICROBIOLOGY

Statistical methods for identifying differentially expressed genes in RNA-Seq experiments

(2012) Zhide Fang et al.   Cell and Bioscience

Polymorphisms of the SLC11A1 gene and resistance to bovine tuberculosis in African Zebu cattle

(2011) H. N. Kadarmideen et al.   ANIMAL GENETICS

Evaluation of the coverage and depth of transcriptome by RNA-Seq in chickens

(2011) Ying Wang et al.   BMC BIOINFORMATICS

Genome-wide transcriptional profiling of peripheral blood leukocytes from cattle infected with Mycobacterium bovis reveals suppression of host immune genes

(2011) Kate E Killick et al.   BMC GENOMICS

Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis

(2011) Alessandro Guida et al.   BMC GENOMICS

A large-scale study of differential gene expression in monocyte-derived macrophages infected with several strains of Mycobacterium avium subspecies paratuberculosis

(2011) E. Kabara et al.   Briefings in Functional Genomics

A comparison of analog and Next-Generation transcriptomic tools for mammalian studies

(2011) N. C. Roy et al.   Briefings in Functional Genomics

An association between TRP64ARG polymorphism of the B3 adrenoreceptor gene and some metabolic disturbances

(2011) Aibek E Mirrakhimov et al.   Cardiovascular Diabetology

Comparing Next-Generation Sequencing and Microarray Technologies in a Toxicological Study of the Effects of Aristolochic Acid on Rat Kidneys

(2011) Zhenqiang Su et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Immunodiagnosis of Tuberculosis: a Dynamic View of Biomarker Discovery

(2011) S. Kunnath-Velayudhan et al.   CLINICAL MICROBIOLOGY REVIEWS

Early response of bovine alveolar macrophages to infection with live and heat-killed Mycobacterium bovis

(2011) Stephanie Widdison et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

RNA-sequence analysis of human B-cells

(2011) J. M. Toung et al.   GENOME RESEARCH

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

Palaeogenomics of Mycobacterium tuberculosis: epidemic bursts with a degrading genome

(2011) Zoheira Djelouadji et al.   LANCET INFECTIOUS DISEASES

Apoptosis is an innate defense function of macrophages against Mycobacterium tuberculosis

(2011) S M Behar et al.   Mucosal Immunology

Deep-Sequencing Analysis of the Mouse Transcriptome Response to Infection with Brucella melitensis Strains of Differing Virulence

(2011) Fangkun Wang et al.   PLoS One

Genome-wide antisense transcription drives mRNA processing in bacteria

(2011) I. Lasa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

What are natural antisense transcripts good for?

(2010) Andreas Werner et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling

(2010) James R Bradford et al.   BMC GENOMICS

Survival mechanisms of pathogenic Mycobacterium tuberculosis H37Rv

(2010) Laxman S. Meena et al.   FEBS Journal

IntracellularMycobacterium aviumIntersect Transferrin in the Rab11+Recycling Endocytic Pathway and Avoid Lipocalin 2 Trafficking to the Lysosomal Pathway

(2010) Øyvind Halaas et al.   JOURNAL OF INFECTIOUS DISEASES

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

Regulation of antigen presentation by Mycobacterium tuberculosis: a role for Toll-like receptors

(2010) Clifford V. Harding et al.   NATURE REVIEWS MICROBIOLOGY

A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species

(2010) Song Liu et al.   NUCLEIC ACIDS RESEARCH

What do natural antisense transcripts regulate?

(2010) Andreas Werner et al.   RNA Biology

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

(2010) Mark D Robinson et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

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

(2009) M. D. Robinson et al.   BIOINFORMATICS

The acute-phase protein serum amyloid A3 is expressed in the bovine mammary gland and plays a role in host defence

(2009) Adrian J. Molenaar et al.   BIOMARKERS

Identification of differentially expressed sense and antisense transcript pairs in breast epithelial tissues

(2009) Anita Grigoriadis et al.   BMC GENOMICS

Naturally occurring antisense RNA: function and mechanisms of action

(2009) Andreas Werner et al.   CURRENT OPINION IN NEPHROLOGY AND HYPERTENSION

Mistargeting of SH3TC2 away from the recycling endosome causes Charcot–Marie–Tooth disease type 4C

(2009) Rhys C. Roberts et al.   HUMAN MOLECULAR GENETICS

RNA-Seq—quantitative measurement of expression through massively parallel RNA-sequencing

(2009) Brian T. Wilhelm et al.   METHODS

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

Regulatory roles of natural antisense transcripts

(2009) Mohammad Ali Faghihi et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

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

(2008) J. C. Marioni et al.   GENOME RESEARCH

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms

(2008) Peter A. C. 't Hoen et al.   NUCLEIC ACIDS RESEARCH

Origin, Spread and Demography of the Mycobacterium tuberculosis Complex

(2008) Thierry Wirth et al.   PLoS Pathogens

ADRB3 Adrenergic Receptor Is a Key Regulator of Human Myometrial Apoptosis and Inflammation During Chorioamnionitis1

(2007) Fréderic Lirussi et al.   BIOLOGY OF REPRODUCTION

Interleukin-17: A novel inflammatory cytokine that bridges innate and adaptive immunity

(2007) Jeffrey et al.   Frontiers in Bioscience-Landmark