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

Gene expression profiling of human breast tissue samples using SAGE-Seq

(2010) Z. J. Wu et al.   GENOME RESEARCH

CD8 T cell response and evolutionary pressure to HIV-1 cryptic epitopes derived from antisense transcription

(2010) Anju Bansal et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Comprehensive comparative analysis of strand-specific RNA sequencing methods

(2010) Joshua Z Levin et al.   NATURE METHODS

Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies

(2010) Osvaldo Zagordi et al.   NUCLEIC ACIDS RESEARCH

HIV Drug Resistance Surveillance Using Pooled Pyrosequencing

(2010) Hezhao Ji et al.   PLoS One

High-Throughput SuperSAGE for Digital Gene Expression Analysis of Multiple Samples Using Next Generation Sequencing

(2010) Hideo Matsumura et al.   PLoS One

Genome-Wide mRNA Expression Correlates of Viral Control in CD4+ T-Cells from HIV-1-Infected Individuals

(2010) Margalida Rotger et al.   PLoS Pathogens

Massively parallel pyrosequencing in HIV research

(2009) Frederic D Bushman et al.   AIDS

Detection of low-frequency pretherapy chemokine (CXC motif) receptor 4 (CXCR4)-using HIV-1 with ultra-deep pyrosequencing

(2009) John Archer et al.   AIDS

HIV-1-infected dendritic cells show 2 phases of gene expression changes, with lysosomal enzyme activity decreased during the second phase

(2009) A. N. Harman et al.   BLOOD

Next-generation tag sequencing for cancer gene expression profiling

(2009) A. S. Morrissy et al.   GENOME RESEARCH

Circulating Monocytes in HIV-1-Infected Viremic Subjects Exhibit an Antiapoptosis Gene Signature and Virus- and Host-Mediated Apoptosis Resistance

(2009) M. S. Giri et al.   JOURNAL OF IMMUNOLOGY

Microarray Analysis of Lymphatic Tissue Reveals Stage-Specific, Gene Expression Signatures in HIV-1 Infection

(2009) Q. Li et al.   JOURNAL OF IMMUNOLOGY

Low-Abundance Drug-Resistant Viral Variants in Chronically HIV-Infected, Antiretroviral Treatment–Naive Patients Significantly Impact Treatment Outcomes

(2009) Birgitte B. Simen et al.   JOURNAL OF INFECTIOUS DISEASES

Gene Expression Profiles of HIV-1-Infected Glia and Brain: Toward Better Understanding of the Role of Astrocytes in HIV-1-Associated Neurocognitive Disorders

(2009) Alejandra Borjabad et al.   Journal of Neuroimmune Pharmacology

The digital generation

(2009) Nathan Blow   NATURE

Pyrosequencing of small non-coding RNAs in HIV-1 infected cells: evidence for the processing of a viral-cellular double-stranded RNA hybrid

(2009) Man Lung Yeung et al.   NUCLEIC ACIDS RESEARCH

Quantitative Deep Sequencing Reveals Dynamic HIV-1 Escape and Large Population Shifts during CCR5 Antagonist Therapy In Vivo

(2009) Athe M. N. Tsibris et al.   PLoS One

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

Massively parallel pyrosequencing highlights minority variants in the HIV-1 env quasispecies deriving from lymphomonocyte sub-populations

(2009) Gabriella Rozera et al.   Retrovirology

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

CD4+ T-Cell Decline after the Interruption of Antiretroviral Therapy in ACTG A5170 Is Predicted by Differential Expression of Genes in the Ras Signaling Pathway

(2008) Maryanne T. Vahey et al.   AIDS RESEARCH AND HUMAN RETROVIRUSES

SuperSAGE: A Modern Platform for Genome-Wide Quantitative Transcript Profiling

(2008) Hideo Matsumura et al.   CURRENT PHARMACEUTICAL BIOTECHNOLOGY

The beginning of the end for microarrays?

(2008) Jay Shendure   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

Cellular Gene Expression Profiles in Rhesus Macaques Challenged Mucosally with a Pathogenic R5 Tropic Simian Human Immunodeficiency Virus Isolate

(2008) Hye-kyung Chung et al.   VIRAL IMMUNOLOGY

Viral Population Estimation Using Pyrosequencing

(2008) Nicholas Eriksson et al.   PLoS Computational Biology