Differentially-Expressed Pseudogenes in HIV-1 Infection

The emerging role of long non-coding RNAs in HIV infection

(2016) Daniel C. Lazar et al.   VIRUS RESEARCH

IL-21 induces antiviral microRNA-29 in CD4 T cells to limit HIV-1 infection

(2015) Stanley Adoro et al.   Nature Communications

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

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

The multilayered complexity of ceRNA crosstalk and competition

(2014) Yvonne Tay et al.   NATURE

Genome-wide mRNA and miRNA analysis of peripheral blood mononuclear cells (PBMC) reveals different miRNAs regulating HIV/HCV co-infection

(2014) P. Gupta et al.   VIROLOGY

The Pan-Cancer analysis of pseudogene expression reveals biologically and clinically relevant tumour subtypes

(2014) Leng Han et al.   Nature Communications

Processed pseudogenes acquired somatically during cancer development

(2014) Susanna L. Cooke et al.   Nature Communications

Differential Expression of Oct4 Variants and Pseudogenes in Normal Urothelium and Urothelial Cancer

(2013) Felix Wezel et al.   AMERICAN JOURNAL OF PATHOLOGY

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

(2013) Yuwen Liu et al.   BIOINFORMATICS

An overview of gene expression dynamics during early ovarian folliculogenesis: specificity of follicular compartments and bi-directional dialog

(2013) Agnes Bonnet et al.   BMC GENOMICS

From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing

(2013) G. K. Marinov et al.   GENOME RESEARCH

Transcribed pseudogene ψPPM1K generates endogenous siRNA to suppress oncogenic cell growth in hepatocellular carcinoma

(2013) Wen-Ling Chan et al.   NUCLEIC ACIDS RESEARCH

Expression Profile of Ectopic Olfactory Receptors Determined by Deep Sequencing

(2013) Caroline Flegel et al.   PLoS One

RNA-Seq Characterization of Spinal Cord Injury Transcriptome in Acute/Subacute Phases: A Resource for Understanding the Pathology at the Systems Level

(2013) Kenian Chen et al.   PLoS One

Integrated transcriptional and competitive endogenous RNA networks are cross-regulated in permissive molecular environments

(2013) U. Ala et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Expressed Pseudogenes in the Transcriptional Landscape of Human Cancers

(2012) Shanker Kalyana-Sundaram et al.   CELL

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Pseudogenes: Newly Discovered Players in Human Cancer

(2012) L. Poliseno   Science Signaling

The GENCODE pseudogene resource

(2012) Baikang Pei et al.   GENOME BIOLOGY

Non-coding RNA and pseudogenes in neurodegenerative diseases: “The (un)Usual Suspects”

(2012) Valerio Costa et al.   Frontiers in Genetics

The association of viral proteins with host cell dynein components during virus infection

(2011) Javier Merino-Gracia et al.   FEBS Journal

Mapping a Dynamic Innate Immunity Protein Interaction Network Regulating Type I Interferon Production

(2011) Shitao Li et al.   IMMUNITY

The HIV-1 gp120/V3 modifies the response of uninfected CD4 T cells to antigen presentation: mapping of the specific transcriptional signature

(2011) Antigone K Morou et al.   Journal of Translational Medicine

Subversion of the actin cytoskeleton during viral infection

(2011) Matthew P. Taylor et al.   NATURE REVIEWS MICROBIOLOGY

HIV DNA is heavily uracilated, which protects it from autointegration

(2011) N. Yan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Functional Role for ADAM10 in Human Immunodeficiency Virus Type-1 Replication

(2011) Brian M Friedrich et al.   Retrovirology

Pseudogenes: Pseudo-functional or key regulators in health and disease?

(2011) R. C. Pink et al.   RNA

A coding-independent function of gene and pseudogene mRNAs regulates tumour biology

(2010) Laura Poliseno et al.   NATURE

Pseudogene-mediated posttranscriptional silencing of HMGA1 can result in insulin resistance and type 2 diabetes

(2010) Eusebio Chiefari et al.   Nature Communications

Biogenesis of small RNAs in animals

(2009) V. Narry Kim et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

TSLP production by epithelial cells exposed to immunodeficiency virus triggers DC-mediated mucosal infection of CD4+ T cells

(2009) D. Fontenot et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes

(2008) Oliver H. Tam et al.   NATURE

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