Next-Generation Sequencing Reveals HIV-1-Mediated Suppression of T Cell Activation and RNA Processing and Regulation of Noncoding RNA Expression in a CD4+ T Cell Line

Analysis of HIV-1 Expression Level and Sense of Transcription by High-Throughput Sequencing of the Infected Cell

(2011) G. Lefebvre et al.   JOURNAL OF VIROLOGY

TDP-43: multiple targets, multiple disease mechanisms?

(2011) Michael Sendtner   NATURE NEUROSCIENCE

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

(2010) James R Bradford et al.   BMC GENOMICS

Identifying potential survival strategies of HIV-1 through virus-host protein interaction networks

(2010) David van Dijk et al.   BMC Systems Biology

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

The cytosolic exonuclease TREX1 inhibits the innate immune response to human immunodeficiency virus type 1

(2010) Nan Yan et al.   NATURE IMMUNOLOGY

The multiple roles of TDP-43 in pre-mRNA processing and gene expression regulation

(2010) Emanuele Buratti et al.   RNA Biology

Unique Signatures of Long Noncoding RNA Expression in Response to Virus Infection and Altered Innate Immune Signaling

(2010) X. Peng et al.   mBio

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

RNA and Disease

(2009) Thomas A. Cooper et al.   CELL

Human Immunodeficiency Virus Type 1 Mediates Global Disruption of Innate Antiviral Signaling and Immune Defenses within Infected Cells

(2009) B. P. Doehle et al.   JOURNAL OF VIROLOGY

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Microarray study reveals that HIV-1 induces rapid type-I interferon-dependent p53 mRNA up-regulation in human primary CD4+ T cells

(2009) Michaël Imbeault et al.   Retrovirology

Host Cell Factors in HIV Replication: Meta-Analysis of Genome-Wide Studies

(2009) Frederic D. Bushman et al.   PLoS Pathogens

Transcriptional Profiling in Pathogenic and Non-Pathogenic SIV Infections Reveals Significant Distinctions in Kinetics and Tissue Compartmentalization

(2009) Sharon Lederer et al.   PLoS Pathogens

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

R5 and X4 HIV Viruses Differentially Modulate Host Gene Expression in Resting CD4+ T Cells

(2008) Mélissa Sirois et al.   AIDS RESEARCH AND HUMAN RETROVIRUSES

Most mammalian mRNAs are conserved targets of microRNAs

(2008) R. C. Friedman et al.   GENOME RESEARCH

Role of Cellular RNA Processing Factors in Human Immunodeficiency Virus Type 1 mRNA Metabolism, Replication, and Infectivity

(2008) J. A. Jablonski et al.   JOURNAL OF VIROLOGY

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

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Distinct Genetic Loci Control Plasma HIV-RNA and Cellular HIV-DNA Levels in HIV-1 Infection: The ANRS Genome Wide Association 01 Study

(2008) Cyril Dalmasso et al.   PLoS One

BCL11B is a general transcriptional repressor of the HIV-1 long terminal repeat in T lymphocytes through recruitment of the NuRD complex

(2008) Valeriu B. Cismasiu et al.   VIROLOGY