Gene activity in primary T cells infected with HIV89.6: intron retention and induction of genomic repeats

HIV-1 Integration Landscape during Latent and Active Infection

(2015) Lillian B. Cohn et al.   CELL

Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells

(2015) Edward J. Grow et al.   NATURE

Modulation of human endogenous retrovirus (HERV) transcription during persistent and de novo HIV-1 infection

(2015) Michelle Vincendeau et al.   Retrovirology

Human endogenous retroviruses sustain complex and cooperative regulation of gene-containing loci and unannotated megabase-sized regions

(2015) Martin Sokol et al.   Retrovirology

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

Comparing DNA integration site clusters with scan statistics

(2014) Charles C. Berry et al.   BIOINFORMATICS

Transcriptional landscape of repetitive elements in normal and cancer human cells

(2014) Steven W Criscione et al.   BMC GENOMICS

Widespread intron retention in mammals functionally tunes transcriptomes

(2014) Ulrich Braunschweig et al.   GENOME RESEARCH

HIV-1 Infection Leads to Increased Transcription of Human Endogenous Retrovirus HERV-K (HML-2) Proviruses In Vivo but Not to Increased Virion Production

(2014) N. Bhardwaj et al.   JOURNAL OF VIROLOGY

Deep Sequencing of HIV-Infected Cells: Insights into Nascent Transcription and Host-Directed Therapy

(2014) X. Peng et al.   JOURNAL OF VIROLOGY

Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells

(2014) Jichang Wang et al.   NATURE

Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance

(2014) Alexandre Fort et al.   NATURE GENETICS

NGS library preparation may generate artifactual integration sites of AAV vectors

(2014) Benjamin Cogné et al.   NATURE MEDICINE

Ribonuclease L and metal-ion–independent endoribonuclease cleavage sites in host and viral RNAs

(2014) Daphne A. Cooper et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

HIV-1 Infection Causes a Down-Regulation of Genes Involved in Ribosome Biogenesis

(2014) Claudia L. Kleinman et al.   PLoS One

MAVS, cGAS, and endogenous retroviruses in T-independent B cell responses

(2014) Ming Zeng et al.   SCIENCE

Proliferation of cells with HIV integrated into cancer genes contributes to persistent infection

(2014) T. A. Wagner et al.   SCIENCE

Specific HIV integration sites are linked to clonal expansion and persistence of infected cells

(2014) F. Maldarelli et al.   SCIENCE

Gene Therapy for Wiskott-Aldrich Syndrome--Long-Term Efficacy and Genotoxicity

(2014) C. J. Braun et al.   Science Translational Medicine

Lack of Detectable HIV-1 Molecular Evolution during Suppressive Antiretroviral Therapy

(2014) Mary F. Kearney et al.   PLoS Pathogens

IVT-seq reveals extreme bias in RNA sequencing

(2014) Nicholas F Lahens et al.   GENOME BIOLOGY

HIV infection reveals widespread expansion of novel centromeric human endogenous retroviruses

(2013) R. Contreras-Galindo et al.   GENOME RESEARCH

LINE-1 Retrotransposable Element DNA Accumulates in HIV-1-Infected Cells

(2013) R. B. Jones et al.   JOURNAL OF VIROLOGY

HIV-1 evades innate immune recognition through specific cofactor recruitment

(2013) Jane Rasaiyaah et al.   NATURE

Interferon-Beta Induces Distinct Gene Expression Response Patterns in Human Monocytes versus T cells

(2013) Noa Henig et al.   PLoS One

Human endogenous retrovirus K (HML-2) RNA and protein expression is a marker for human embryonic and induced pluripotent stem cells

(2013) Nina V Fuchs et al.   Retrovirology

HIV latency and integration site placement in five cell-based models

(2013) Scott Sherrill-Mix et al.   Retrovirology

IFI16 DNA Sensor Is Required for Death of Lymphoid CD4 T Cells Abortively Infected with HIV

(2013) K. M. Monroe et al.   SCIENCE

Cyclic GMP-AMP Synthase Is an Innate Immune Sensor of HIV and Other Retroviruses

(2013) D. Gao et al.   SCIENCE

In-Depth Analysis of the Interaction of HIV-1 with Cellular microRNA Biogenesis and Effector Mechanisms

(2013) A. W. Whisnant et al.   mBio

Next-Generation Sequencing of Small RNAs from HIV-Infected Cells Identifies Phased microRNA Expression Patterns and Candidate Novel microRNAs Differentially Expressed upon Infection

(2013) S. T. Chang et al.   mBio

24 Hours in the Life of HIV-1 in a T Cell Line

(2013) Pejman Mohammadi et al.   PLoS Pathogens

Synergistic Effects of Interleukin-7 and Pre-T Cell Receptor Signaling in Human T Cell Development

(2012) Ekta S. Patel et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Whole transcriptome characterization of aberrant splicing events induced by lentiviral vector integrations

(2012) Daniela Cesana et al.   JOURNAL OF CLINICAL INVESTIGATION

HERV-K–specific T cells eliminate diverse HIV-1/2 and SIV primary isolates

(2012) R. Brad Jones et al.   JOURNAL OF CLINICAL INVESTIGATION

Lentiviral vector integration in the human genome induces alternative splicing and generates aberrant transcripts

(2012) Arianna Moiani et al.   JOURNAL OF CLINICAL INVESTIGATION

Suppression of ribosomal protein synthesis and protein translation factors by Peg-interferon alpha/ribavirin in HCV patients blood mononuclear cells (PBMC)

(2012) Rahul Gupta et al.   Journal of Translational Medicine

An Increasing Proportion of Monotypic HIV-1 DNA Sequences during Antiretroviral Treatment Suggests Proliferation of HIV-Infected Cells

(2012) Thor A. Wagner et al.   JOURNAL OF VIROLOGY

INTERFEROME v2.0: an updated database of annotated interferon-regulated genes

(2012) Irina Rusinova et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Karin Breuer et al.   NUCLEIC ACIDS RESEARCH

Dynamic regulation of HIV-1 mRNA populations analyzed by single-molecule enrichment and long-read sequencing

(2012) Karen E. Ocwieja et al.   NUCLEIC ACIDS RESEARCH

High Accuracy Mutation Detection in Leukemia on a Selected Panel of Cancer Genes

(2012) Zeynep Kalender Atak et al.   PLoS One

HERV-H RNA is abundant in human embryonic stem cells and a precise marker for pluripotency

(2012) Federico A Santoni et al.   Retrovirology

Landscape of Somatic Retrotransposition in Human Cancers

(2012) E. Lee et al.   SCIENCE

Exon Level Transcriptomic Profiling of HIV-1-Infected CD4+ T Cells Reveals Virus-Induced Genes and Host Environment Favorable for Viral Replication

(2012) Michaël Imbeault et al.   PLoS Pathogens

Comparative transcriptomics of extreme phenotypes of human HIV-1 infection and SIV infection in sooty mangabey and rhesus macaque

(2011) Margalida Rotger et al.   JOURNAL OF CLINICAL INVESTIGATION

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

Identification of Human Endogenous Retrovirus-Specific T Cell Responses in Vertically HIV-1-Infected Subjects

(2011) R. Tandon et al.   JOURNAL OF VIROLOGY

Strong Human Endogenous Retrovirus-Specific T Cell Responses Are Associated with Control of HIV-1 in Chronic Infection

(2011) D. SenGupta et al.   JOURNAL OF VIROLOGY

Identification, characterization, and comparative genomic distribution of the HERV-K (HML-2) group of human endogenous retroviruses

(2011) Ravi P Subramanian et al.   Retrovirology

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

(2011) S. T. Chang et al.   mBio

UniProt Knowledgebase: a hub of integrated protein data

(2011) M. Magrane et al.   Database-The Journal of Biological Databases and Curation

Identification of Unusual and Novel HIV Type 1 Spliced Transcripts Generated in Vivo

(2010) Cristina Carrera et al.   AIDS RESEARCH AND HUMAN RETROVIRUSES

Natural Mutagenesis of Human Genomes by Endogenous Retrotransposons

(2010) Rebecca C. Iskow et al.   CELL

Regulatory divergence in Drosophila revealed by mRNA-seq

(2010) C. J. McManus et al.   GENOME RESEARCH

P-TEFb Kinase Complex Phosphorylates Histone H1 to Regulate Expression of Cellular and HIV-1 Genes

(2010) Siobhan K. O'Brien et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Host Genes Associated with HIV-1 Replication in Lymphatic Tissue

(2010) A. J. Smith et al.   JOURNAL OF IMMUNOLOGY

Transfusion independence and HMGA2 activation after gene therapy of human β-thalassaemia

(2010) Marina Cavazzana-Calvo et al.   NATURE

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Apparent Non-Canonical Trans-Splicing Is Generated by Reverse Transcriptase In Vitro

(2010) Jonathan Houseley et al.   PLoS One

Current Estimates for HIV-1 Production Imply Rapid Viral Clearance in Lymphoid Tissues

(2010) Rob J. De Boer et al.   PLoS Computational Biology

Controlling Cellular P-TEFb Activity by the HIV-1 Transcriptional Transactivator Tat

(2010) Lisa Muniz et al.   PLoS Pathogens

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

(2010) Margalida Rotger et al.   PLoS Pathogens

HIV integration site distributions in resting and activated CD4+ T cells infected in culture

(2009) Troy Brady et al.   AIDS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Integration target site selection by a resurrected human endogenous retrovirus

(2009) T. Brady et al.   GENES & DEVELOPMENT

Human Immunodeficiency Virus Type 1 (HIV-1) Induces the Cytoplasmic Retention of Heterogeneous Nuclear Ribonucleoprotein A1 by Disrupting Nuclear Import

(2009) Anne Monette et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

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

Analysis of Human Immunodeficiency Virus Type 1 Viremia and Provirus in Resting CD4+ T Cells Reveals a Novel Source of Residual Viremia in Patients on Antiretroviral Therapy

(2009) T. P. Brennan et al.   JOURNAL OF VIROLOGY

RNase L downmodulation of the RNA-binding protein, HuR and cellular growth

(2009) W Al-Ahmadi et al.   ONCOGENE

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

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Insertional oncogenesis in 4 patients after retrovirus-mediated gene therapy of SCID-X1

(2008) Salima Hacein-Bey-Abina et al.   JOURNAL OF CLINICAL INVESTIGATION

HIV rebounds from latently infected cells, rather than from continuing low-level replication

(2008) B. Joos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

HIV-1 infection induces changes in expression of cellular splicing factors that regulate alternative viral splicing and virus production in macrophages

(2008) Dinushka Dowling et al.   Retrovirology

Transcriptional profiles in CD8+ T cells from HIV+ progressors on HAART are characterized by coordinated up-regulation of oxidative phosphorylation enzymes and interferon responses

(2008) Jing Qin Wu et al.   VIROLOGY