Ago HITS-CLIP expands understanding of Kaposi's sarcoma-associated herpesvirus miRNA function in primary effusion lymphomas.

PubWeight™: 1.53‹?› | Rank: Top 4%

🔗 View Article (PMC 3426530)

Published in PLoS Pathog on August 23, 2012

Authors

Irina Haecker1, Lauren A Gay, Yajie Yang, Jianhong Hu, Alison M Morse, Lauren M McIntyre, Rolf Renne

Author Affiliations

1: Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, United States of America.

Articles citing this

Hepatitis C virus RNA functionally sequesters miR-122. Cell (2015) 2.04

Virus-encoded microRNAs: an overview and a look to the future. PLoS Pathog (2012) 1.80

Kaposi's sarcoma herpesvirus microRNAs induce metabolic transformation of infected cells. PLoS Pathog (2014) 1.61

MicroRNAs as mediators of viral evasion of the immune system. Nat Immunol (2013) 1.52

Argonaute-associated short introns are a novel class of gene regulators. Nat Commun (2016) 1.40

Identification of a pan-cancer oncogenic microRNA superfamily anchored by a central core seed motif. Nat Commun (2013) 1.19

Virus meets host microRNA: the destroyer, the booster, the hijacker. Mol Cell Biol (2014) 1.14

Transcriptome-wide discovery of microRNA binding sites in human brain. Neuron (2014) 1.13

γ-Herpesvirus-encoded miRNAs and their roles in viral biology and pathogenesis. Curr Opin Virol (2013) 1.10

Widespread context dependency of microRNA-mediated regulation. Genome Res (2014) 1.08

Virus-encoded microRNAs facilitate gammaherpesvirus latency and pathogenesis in vivo. MBio (2014) 1.04

Systemically circulating viral and tumor-derived microRNAs in KSHV-associated malignancies. PLoS Pathog (2013) 1.04

Viral noncoding RNAs: more surprises. Genes Dev (2015) 0.99

Kaposi sarcoma associated herpesvirus pathogenesis (KSHV)--an update. Curr Opin Virol (2013) 0.99

Comprehensive miRNA sequence analysis reveals survival differences in diffuse large B-cell lymphoma patients. Genome Biol (2015) 0.99

Comprehensive proteomic profiling identifies the androgen receptor axis and other signaling pathways as targets of microRNAs suppressed in metastatic prostate cancer. Oncogene (2015) 0.95

Argonaute CLIP-Seq reveals miRNA targetome diversity across tissue types. Sci Rep (2014) 0.94

Design and bioinformatics analysis of genome-wide CLIP experiments. Nucleic Acids Res (2015) 0.88

Kaposi's sarcoma-associated herpesvirus microRNA single-nucleotide polymorphisms identified in clinical samples can affect microRNA processing, level of expression, and silencing activity. J Virol (2013) 0.88

Proteomic screening of human targets of viral microRNAs reveals functions associated with immune evasion and angiogenesis. PLoS Pathog (2013) 0.88

Latency locus complements MicroRNA 155 deficiency in vivo. J Virol (2013) 0.88

Divergent MicroRNA targetomes of closely related circulating strains of a polyomavirus. J Virol (2013) 0.87

Genomewide mapping and screening of Kaposi's sarcoma-associated herpesvirus (KSHV) 3' untranslated regions identify bicistronic and polycistronic viral transcripts as frequent targets of KSHV microRNAs. J Virol (2013) 0.87

Kaposi's sarcoma-associated herpesvirus encodes a mimic of cellular miR-23. J Virol (2013) 0.87

A Broad RNA Virus Survey Reveals Both miRNA Dependence and Functional Sequestration. Cell Host Microbe (2016) 0.86

KSHV miRNAs decrease expression of lytic genes in latently infected PEL and endothelial cells by targeting host transcription factors. Viruses (2014) 0.85

The Role of microRNAs in the Pathogenesis of Herpesvirus Infection. Viruses (2016) 0.85

MicroRNA Target Recognition: Insights from Transcriptome-Wide Non-Canonical Interactions. Mol Cells (2016) 0.84

A KSHV microRNA Directly Targets G Protein-Coupled Receptor Kinase 2 to Promote the Migration and Invasion of Endothelial Cells by Inducing CXCR2 and Activating AKT Signaling. PLoS Pathog (2015) 0.84

A Toolbox for Herpesvirus miRNA Research: Construction of a Complete Set of KSHV miRNA Deletion Mutants. Viruses (2016) 0.84

Kaposi sarcoma-associated herpesvirus: immunobiology, oncogenesis, and therapy. J Clin Invest (2016) 0.82

Systematic microRNA analysis identifies ATP6V0C as an essential host factor for human cytomegalovirus replication. PLoS Pathog (2013) 0.82

Kaposi's Sarcoma-Associated Herpesvirus (KSHV) Induces the Oncogenic miR-17-92 Cluster and Down-Regulates TGF-β Signaling. PLoS Pathog (2015) 0.81

Kaposi's sarcoma-associated herpesvirus-positive primary effusion lymphoma tumor formation in NOD/SCID mice is inhibited by neomycin and neamine blocking angiogenin's nuclear translocation. J Virol (2013) 0.81

Leveraging biological replicates to improve analysis in ChIP-seq experiments. Comput Struct Biotechnol J (2014) 0.80

Tiny giants of gene regulation: experimental strategies for microRNA functional studies. Wiley Interdiscip Rev Dev Biol (2016) 0.80

Analysis of the mRNA targetome of microRNAs expressed by Marek's disease virus. MBio (2014) 0.79

Viral miRNA targeting of bicistronic and polycistronic transcripts. Curr Opin Virol (2014) 0.79

Intramolecular circularization increases efficiency of RNA sequencing and enables CLIP-Seq of nuclear RNA from human cells. Nucleic Acids Res (2015) 0.79

PATZ1 is a target of miR-29b that is induced by Ha-Ras oncogene in rat thyroid cells. Sci Rep (2016) 0.78

HITS-CLIP and PAR-CLIP advance viral miRNA targetome analysis. Crit Rev Eukaryot Gene Expr (2014) 0.78

Viral microRNA genomics and target validation. Curr Opin Virol (2014) 0.78

Dissecting the expression relationships between RNA-binding proteins and their cognate targets in eukaryotic post-transcriptional regulatory networks. Sci Rep (2016) 0.78

Viral microRNAs Target a Gene Network, Inhibit STAT Activation, and Suppress Interferon Responses. Sci Rep (2017) 0.77

Next-Generation Sequencing Analysis Reveals Differential Expression Profiles of MiRNA-mRNA Target Pairs in KSHV-Infected Cells. PLoS One (2015) 0.77

MicroRNAs Expressed during Viral Infection: Biomarker Potential and Therapeutic Considerations. Biomark Insights (2016) 0.77

Kaposi's sarcoma herpesvirus (KSHV) microRNA K12-1 functions as an oncogene by activating NF-κB/IL-6/STAT3 signaling. Oncotarget (2016) 0.77

Complexities of gammaherpesvirus transcription revealed by microarrays and RNAseq. Curr Opin Virol (2013) 0.77

Retracted Pan-viral-microRNA screening identifies interferon inhibition as a common function of diverse viruses. Proc Natl Acad Sci U S A (2015) 0.77

Chromatinization of the KSHV Genome During the KSHV Life Cycle. Cancers (Basel) (2015) 0.77

Endothelial and circulating C19MC microRNAs are biomarkers of infantile hemangioma. JCI Insight (2016) 0.76

Bovine Leukemia Virus Small Noncoding RNAs Are Functional Elements That Regulate Replication and Contribute to Oncogenesis In Vivo. PLoS Pathog (2016) 0.76

Epstein-Barr viral microRNAs target caspase 3. Virol J (2016) 0.76

How do viruses trick B cells into becoming lymphomas? Curr Opin Hematol (2014) 0.76

A systems biology approach identified different regulatory networks targeted by KSHV miR-K12-11 in B cells and endothelial cells. BMC Genomics (2014) 0.76

A KSHV microRNA enhances viral latency and induces angiogenesis by targeting GRK2 to activate the CXCR2/AKT pathway. Oncotarget (2016) 0.76

In Silico Characterization of miRNA and Long Non-Coding RNA Interplay in Multiple Myeloma. Genes (Basel) (2016) 0.75

Next-Generation Sequencing in the Understanding of Kaposi's Sarcoma-Associated Herpesvirus (KSHV) Biology. Viruses (2016) 0.75

Virus-Mediated Alterations in miRNA Factors and Degradation of Viral miRNAs by MCPIP1. PLoS Biol (2016) 0.75

Improvements to the HITS-CLIP protocol eliminate widespread mispriming artifacts. BMC Genomics (2016) 0.75

KSHV microRNAs Target GADD45B to Protect Infected Cells from Cell Cycle Arrest and Apoptosis. J Virol (2016) 0.75

Experimental procedures to identify and validate specific mRNA targets of miRNAs. EXCLI J (2015) 0.75

The Landscape of microRNA Targeting in Prostate Cancer Defined by AGO-PAR-CLIP. Neoplasia (2016) 0.75

The small noncoding RNAs (sncRNAs) of murine gammaherpesvirus 68 (MHV-68) are involved in regulating the latent-to-lytic switch in vivo. Sci Rep (2016) 0.75

Up-regulation of tumor suppressor genes by exogenous dhC16-Cer contributes to its anti-cancer activity in primary effusion lymphoma. Oncotarget (2017) 0.75

microRNA dependent and independent deregulation of long non-coding RNAs by an oncogenic herpesvirus. PLoS Pathog (2017) 0.75

Herpesviruses shape tumour microenvironment through exosomal transfer of viral microRNAs. PLoS Pathog (2017) 0.75

Articles cited by this

Statistical methods for assessing agreement between two methods of clinical measurement. Lancet (1986) 211.50

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc (2009) 137.99

Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods (2008) 126.81

The functions of animal microRNAs. Nature (2004) 64.85

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res (2008) 54.83

On the origin of cancer cells. Science (1956) 49.55

MicroRNA signatures in human cancers. Nat Rev Cancer (2006) 46.29

Identification of herpesvirus-like DNA sequences in AIDS-associated Kaposi's sarcoma. Science (1994) 39.60

MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell (2007) 38.42

The impact of microRNAs on protein output. Nature (2008) 32.39

Widespread changes in protein synthesis induced by microRNAs. Nature (2008) 31.44

NF-kappaB-dependent induction of microRNA miR-146, an inhibitor targeted to signaling proteins of innate immune responses. Proc Natl Acad Sci U S A (2006) 21.58

Kaposi's sarcoma-associated herpesvirus-like DNA sequences in AIDS-related body-cavity-based lymphomas. N Engl J Med (1995) 21.16

Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell (2010) 17.87

Kaposi's sarcoma-associated herpesvirus-like DNA sequences in multicentric Castleman's disease. Blood (1995) 16.81

Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature (2009) 14.07

Identification of microRNAs of the herpesvirus family. Nat Methods (2005) 12.98

Identification of virus-encoded microRNAs. Science (2004) 12.56

Pre-B cell proliferation and lymphoblastic leukemia/high-grade lymphoma in E(mu)-miR155 transgenic mice. Proc Natl Acad Sci U S A (2006) 10.65

Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol (2008) 10.17

Sustained expression of microRNA-155 in hematopoietic stem cells causes a myeloproliferative disorder. J Exp Med (2008) 5.97

Kaposi's sarcoma-associated herpesvirus expresses an array of viral microRNAs in latently infected cells. Proc Natl Acad Sci U S A (2005) 5.88

Host immune system gene targeting by a viral miRNA. Science (2007) 5.10

A viral microRNA functions as an orthologue of cellular miR-155. Nature (2007) 5.09

Dynamics of cadherin/catenin complex formation: novel protein interactions and pathways of complex assembly. J Cell Biol (1994) 5.03

A combined computational and microarray-based approach identifies novel microRNAs encoded by human gamma-herpesviruses. RNA (2006) 4.47

Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans. Nat Struct Mol Biol (2010) 4.22

Kaposi's sarcoma-associated herpesvirus encodes an ortholog of miR-155. J Virol (2007) 4.19

A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins. Nat Methods (2011) 4.06

Tumor protein 53-induced nuclear protein 1 expression is repressed by miR-155, and its restoration inhibits pancreatic tumor development. Proc Natl Acad Sci U S A (2007) 4.04

Cloning and identification of a microRNA cluster within the latency-associated region of Kaposi's sarcoma-associated herpesvirus. J Virol (2005) 4.01

MicroRNA-155 modulates the interleukin-1 signaling pathway in activated human monocyte-derived dendritic cells. Proc Natl Acad Sci U S A (2009) 3.97

MicroRNAs can generate thresholds in target gene expression. Nat Genet (2011) 3.90

Diverse herpesvirus microRNAs target the stress-induced immune ligand MICB to escape recognition by natural killer cells. Cell Host Microbe (2009) 3.59

Viruses, microRNAs, and host interactions. Annu Rev Microbiol (2010) 3.30

Identification of cellular genes targeted by KSHV-encoded microRNAs. PLoS Pathog (2007) 3.16

Interleukin (IL)-10 inhibits nuclear factor kappa B (NF kappa B) activation in human monocytes. IL-10 and IL-4 suppress cytokine synthesis by different mechanisms. J Biol Chem (1995) 2.95

Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs. Nat Struct Mol Biol (2011) 2.85

Src homology 2 domain-containing inositol-5-phosphatase and CCAAT enhancer-binding protein beta are targeted by miR-155 in B cells of Emicro-MiR-155 transgenic mice. Blood (2009) 2.68

Kinetic analysis reveals the fate of a microRNA following target regulation in mammalian cells. Curr Biol (2011) 2.53

The viral and cellular microRNA targetome in lymphoblastoid cell lines. PLoS Pathog (2012) 2.45

MicroRNA-155 is an Epstein-Barr virus-induced gene that modulates Epstein-Barr virus-regulated gene expression pathways. J Virol (2008) 2.45

Tandem array-based expression screens identify host mRNA targets of virus-encoded microRNAs. Nat Genet (2008) 2.42

KSHV vFLIP is essential for the survival of infected lymphoma cells. J Exp Med (2004) 2.39

A viral protein that selectively downregulates ICAM-1 and B7-2 and modulates T cell costimulation. J Clin Invest (2001) 2.36

Regulation of NF-kappaB inhibitor IkappaBalpha and viral replication by a KSHV microRNA. Nat Cell Biol (2010) 2.33

Viral homologs of BCL-2: role of apoptosis in the regulation of virus infection. Genes Dev (2002) 2.29

Btf, a novel death-promoting transcriptional repressor that interacts with Bcl-2-related proteins. Mol Cell Biol (1999) 2.22

RNA-seq: technical variability and sampling. BMC Genomics (2011) 2.19

A multifunctional human Argonaute2-specific monoclonal antibody. RNA (2008) 2.17

Conservation of virally encoded microRNAs in Kaposi sarcoma--associated herpesvirus in primary effusion lymphoma cell lines and in patients with Kaposi sarcoma or multicentric Castleman disease. J Infect Dis (2007) 2.17

Regulation of KSHV lytic switch protein expression by a virus-encoded microRNA: an evolutionary adaptation that fine-tunes lytic reactivation. Cell Host Microbe (2009) 2.15

A novel monoclonal antibody against human Argonaute proteins reveals unexpected characteristics of miRNAs in human blood cells. RNA (2007) 2.13

Viral microRNA targetome of KSHV-infected primary effusion lymphoma cell lines. Cell Host Microbe (2011) 2.13

Identification and remediation of biases in the activity of RNA ligases in small-RNA deep sequencing. Nucleic Acids Res (2011) 2.01

Epigenetic regulation of Kaposi's sarcoma-associated herpesvirus latency by virus-encoded microRNAs that target Rta and the cellular Rbl2-DNMT pathway. J Virol (2010) 1.98

Mutator activity induced by microRNA-155 (miR-155) links inflammation and cancer. Proc Natl Acad Sci U S A (2011) 1.96

Systematic analysis of viral and cellular microRNA targets in cells latently infected with human gamma-herpesviruses by RISC immunoprecipitation assay. Cell Host Microbe (2010) 1.91

EBV and human microRNAs co-target oncogenic and apoptotic viral and human genes during latency. EMBO J (2012) 1.91

Mouse cytomegalovirus microRNAs dominate the cellular small RNA profile during lytic infection and show features of posttranscriptional regulation. J Virol (2007) 1.90

In-depth analysis of Kaposi's sarcoma-associated herpesvirus microRNA expression provides insights into the mammalian microRNA-processing machinery. J Virol (2009) 1.90

Roles of small RNAs in tumor formation. Trends Mol Med (2010) 1.89

CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins. Nucleic Acids Res (2010) 1.88

Kaposi's sarcoma-associated herpesvirus-infected primary effusion lymphoma has a plasma cell gene expression profile. Proc Natl Acad Sci U S A (2003) 1.84

The impact of miRNA target sites in coding sequences and in 3'UTRs. PLoS One (2011) 1.82

miR-221 and miR-155 regulate human dendritic cell development, apoptosis, and IL-12 production through targeting of p27kip1, KPC1, and SOCS-1. Blood (2011) 1.73

miR-155 and its star-form partner miR-155* cooperatively regulate type I interferon production by human plasmacytoid dendritic cells. Blood (2010) 1.71

Induction of the Warburg effect by Kaposi's sarcoma herpesvirus is required for the maintenance of latently infected endothelial cells. Proc Natl Acad Sci U S A (2010) 1.65

The latency-associated nuclear antigen of Kaposi's sarcoma-associated herpesvirus modulates cellular gene expression and protects lymphoid cells from p16 INK4A-induced cell cycle arrest. J Biol Chem (2004) 1.64

Pre-micro RNA signatures delineate stages of endothelial cell transformation in Kaposi sarcoma. PLoS Pathog (2009) 1.53

Regulation of tumor necrosis factor-like weak inducer of apoptosis receptor protein (TWEAKR) expression by Kaposi's sarcoma-associated herpesvirus microRNA prevents TWEAK-induced apoptosis and inflammatory cytokine expression. J Virol (2010) 1.51

KSHV-encoded miRNAs target MAF to induce endothelial cell reprogramming. Genes Dev (2010) 1.48

Immunoglobulin VH gene mutational analysis suggests that primary effusion lymphomas derive from different stages of B cell maturation. Am J Pathol (1998) 1.46

Array-based transcript profiling and limiting-dilution reverse transcription-PCR analysis identify additional latent genes in Kaposi's sarcoma-associated herpesvirus. J Virol (2010) 1.42

Role of virus-encoded microRNAs in herpesvirus biology. Trends Microbiol (2009) 1.41

Transcriptome and targetome analysis in MIR155 expressing cells using RNA-seq. RNA (2010) 1.39

Gene alteration and precursor and mature microRNA transcription changes contribute to the miRNA signature of primary effusion lymphoma. Blood (2007) 1.34

MicroRNAs encoded by Kaposi's sarcoma-associated herpesvirus regulate viral life cycle. EMBO Rep (2010) 1.34

Kaposi's sarcoma herpesvirus microRNAs target caspase 3 and regulate apoptosis. PLoS Pathog (2011) 1.33

Distinct subsets of primary effusion lymphoma can be identified based on their cellular gene expression profile and viral association. J Virol (2005) 1.30

Multiple endocytic trafficking pathways of MHC class I molecules induced by a Herpesvirus protein. EMBO J (2002) 1.23

Characterization of viral and human RNAs smaller than canonical MicroRNAs. J Virol (2009) 1.23

A Kaposi's sarcoma-associated herpesvirus-encoded ortholog of microRNA miR-155 induces human splenic B-cell expansion in NOD/LtSz-scid IL2Rγnull mice. J Virol (2011) 1.22

Kaposi's sarcoma-associated herpesvirus-encoded microRNA miR-K12-11 attenuates transforming growth factor beta signaling through suppression of SMAD5. J Virol (2011) 1.15

RNA editing of the human herpesvirus 8 kaposin transcript eliminates its transforming activity and is induced during lytic replication. J Virol (2007) 1.11

Tumor suppressor microRNAs are underrepresented in primary effusion lymphoma and Kaposi sarcoma. Blood (2009) 1.09

KSHV viral cyclin inactivates p27KIP1 through Ser10 and Thr187 phosphorylation in proliferating primary effusion lymphomas. Blood (2005) 1.07

Phosphorylation of the cyclin-dependent kinase inhibitor p21Cip1 on serine 130 is essential for viral cyclin-mediated bypass of a p21Cip1-imposed G1 arrest. Mol Cell Biol (2006) 1.05

Viral miRNAs and immune evasion. Biochim Biophys Acta (2011) 1.02

Immunoglobulin V region gene use and structure suggest antigen selection in AIDS-related primary effusion lymphomas. Leukemia (1999) 1.01

Misleading statistics: errors in textbooks, software and manuals. Int J Epidemiol (1988) 0.96

Nuclear factor (NF)-κB controls expression of the immunoregulatory glycan-binding protein galectin-1. Mol Immunol (2011) 0.87

Articles by these authors

Kaposi's sarcoma-associated herpesvirus encodes an ortholog of miR-155. J Virol (2007) 4.19

Cloning and identification of a microRNA cluster within the latency-associated region of Kaposi's sarcoma-associated herpesvirus. J Virol (2005) 4.01

The Arabidopsis F-box protein SLEEPY1 targets gibberellin signaling repressors for gibberellin-induced degradation. Plant Cell (2004) 3.21

Identification of cellular genes targeted by KSHV-encoded microRNAs. PLoS Pathog (2007) 3.16

Della proteins and gibberellin-regulated seed germination and floral development in Arabidopsis. Plant Physiol (2004) 2.95

Persistent bacteremia due to methicillin-resistant Staphylococcus aureus infection is associated with agr dysfunction and low-level in vitro resistance to thrombin-induced platelet microbicidal protein. J Infect Dis (2004) 2.83

Common pattern of evolution of gene expression level and protein sequence in Drosophila. Mol Biol Evol (2004) 2.66

The chemical interactions underlying tomato flavor preferences. Curr Biol (2012) 2.61

PIL5, a phytochrome-interacting bHLH protein, regulates gibberellin responsiveness by binding directly to the GAI and RGA promoters in Arabidopsis seeds. Plant Cell (2007) 2.52

The latency-associated nuclear antigen of Kaposi's sarcoma-associated herpesvirus supports latent DNA replication in dividing cells. J Virol (2002) 2.32

Latency-associated nuclear antigen (LANA) cooperatively binds to two sites within the terminal repeat, and both sites contribute to the ability of LANA to suppress transcription and to facilitate DNA replication. J Biol Chem (2002) 2.21

RNA-seq: technical variability and sampling. BMC Genomics (2011) 2.19

Conservation of virally encoded microRNAs in Kaposi sarcoma--associated herpesvirus in primary effusion lymphoma cell lines and in patients with Kaposi sarcoma or multicentric Castleman disease. J Infect Dis (2007) 2.17

Potential associations between hematogenous complications and bacterial genotype in Staphylococcus aureus infection. J Infect Dis (2007) 2.00

Epigenetic regulation of Kaposi's sarcoma-associated herpesvirus latency by virus-encoded microRNAs that target Rta and the cellular Rbl2-DNMT pathway. J Virol (2010) 1.98

The latency-associated nuclear antigen of Kaposi's sarcoma-associated herpesvirus modulates cellular gene expression and protects lymphoid cells from p16 INK4A-induced cell cycle arrest. J Biol Chem (2004) 1.64

Differential gene expression in response to hydrogen peroxide and the putative PerR regulon of Synechocystis sp. strain PCC 6803. J Bacteriol (2004) 1.64

Long-term-infected telomerase-immortalized endothelial cells: a model for Kaposi's sarcoma-associated herpesvirus latency in vitro and in vivo. J Virol (2006) 1.63

Scarecrow-like 3 promotes gibberellin signaling by antagonizing master growth repressor DELLA in Arabidopsis. Proc Natl Acad Sci U S A (2011) 1.61

Successful range-expanding plants experience less above-ground and below-ground enemy impact. Nature (2008) 1.60

Microarray analysis of the genome-wide response to iron deficiency and iron reconstitution in the cyanobacterium Synechocystis sp. PCC 6803. Plant Physiol (2003) 1.53

KSHV LANA inhibits TGF-beta signaling through epigenetic silencing of the TGF-beta type II receptor. Blood (2008) 1.52

Powdery mildew induces defense-oriented reprogramming of the transcriptome in a susceptible but not in a resistant grapevine. Plant Physiol (2007) 1.50

KSHV-encoded miRNAs target MAF to induce endothelial cell reprogramming. Genes Dev (2010) 1.48

Role of virus-encoded microRNAs in herpesvirus biology. Trends Microbiol (2009) 1.41

Allele-specific expression assays using Solexa. BMC Genomics (2009) 1.41

Regulatory divergence in Drosophila melanogaster and D. simulans, a genomewide analysis of allele-specific expression. Genetics (2009) 1.40

Biological characterization and next-generation genome sequencing of the unclassified Cotia virus SPAn232 (Poxviridae). J Virol (2012) 1.33

Upregulation of xCT by KSHV-encoded microRNAs facilitates KSHV dissemination and persistence in an environment of oxidative stress. PLoS Pathog (2010) 1.30

Sex-specific splicing in Drosophila: widespread occurrence, tissue specificity and evolutionary conservation. Genetics (2008) 1.30

Peripheral myelin protein 22 is regulated post-transcriptionally by miRNA-29a. Glia (2009) 1.22

A Kaposi's sarcoma-associated herpesvirus-encoded ortholog of microRNA miR-155 induces human splenic B-cell expansion in NOD/LtSz-scid IL2Rγnull mice. J Virol (2011) 1.22

Cis and trans regulatory effects contribute to natural variation in transcriptome of Drosophila melanogaster. Mol Biol Evol (2007) 1.22

Viral miRNAs: tools for immune evasion. Curr Opin Microbiol (2010) 1.22

Simpler mode of inheritance of transcriptional variation in male Drosophila melanogaster. Proc Natl Acad Sci U S A (2007) 1.17

Genotype-phenotype mapping in a post-GWAS world. Trends Genet (2012) 1.16

Characterization of the minimal replicator of Kaposi's sarcoma-associated herpesvirus latent origin. J Virol (2005) 1.16

Regulation and autoregulation of the promoter for the latency-associated nuclear antigen of Kaposi's sarcoma-associated herpesvirus. J Biol Chem (2004) 1.14

Data: the foundation of science. Genetics (2010) 1.14

Prognostic significance of molecular genetic aberrations on chromosome segment 11p15.5 in non-small-cell lung cancer. J Clin Oncol (2002) 1.12

SOLiD sequencing of four Vibrio vulnificus genomes enables comparative genomic analysis and identification of candidate clade-specific virulence genes. BMC Genomics (2010) 1.10

γ-Herpesvirus-encoded miRNAs and their roles in viral biology and pathogenesis. Curr Opin Virol (2013) 1.10

Polymorphisms in fibronectin binding protein A of Staphylococcus aureus are associated with infection of cardiovascular devices. Proc Natl Acad Sci U S A (2011) 1.08

Model selection in binary trait locus mapping. Genetics (2005) 1.07

Facilitating discovery: the role of Society Journals in collaborative science. Genetics (2012) 1.07

Nematode-induced changes of transporter gene expression in Arabidopsis roots. Mol Plant Microbe Interact (2005) 1.05

Transcript profiles of the cytokinin response regulator gene family in Populus imply diverse roles in plant development. New Phytol (2007) 1.03

The cytokinin type-B response regulator PtRR13 is a negative regulator of adventitious root development in Populus. Plant Physiol (2009) 1.02

Viral miRNAs and immune evasion. Biochim Biophys Acta (2011) 1.02

Evolution of gene expression in the Drosophila olfactory system. Mol Biol Evol (2008) 1.01

Differential expression of genes important for adaptation in Capsella bursa-pastoris (Brassicaceae). Plant Physiol (2007) 1.01

Isolation and characterization of cul1-7, a recessive allele of CULLIN1 that disrupts SCF function at the C terminus of CUL1 in Arabidopsis thaliana. Genetics (2008) 1.00

Defining gene and QTL networks. Curr Opin Plant Biol (2009) 1.00

Potential associations between severity of infection and the presence of virulence-associated genes in clinical strains of Staphylococcus aureus. PLoS One (2011) 0.99

Nonflowering plants possess a unique folate-dependent phenylalanine hydroxylase that is localized in chloroplasts. Plant Cell (2010) 0.99

Phenotypic plasticity in cell walls of maize brown midrib mutants is limited by lignin composition. J Exp Bot (2010) 0.98

Sex- and segment-specific modulation of gene expression profiles in Drosophila. Dev Biol (2005) 0.97

Genetic dissection of fusiform rust and pitch canker disease traits in loblolly pine. Theor Appl Genet (2005) 0.95

Viral miRNAs. Methods Mol Biol (2011) 0.94

Evolution and diversity of invertase genes in Populus trichocarpa. Planta (2007) 0.94

Transcriptome profiling of embryonic development rate in rainbow trout advanced backcross introgression lines. Mar Biotechnol (NY) (2010) 0.94

Therapeutic challenges of AIDS-related non-Hodgkin's lymphoma in the United States and East Africa. J Natl Cancer Inst (2002) 0.94

Mutational analysis of the latency-associated nuclear antigen DNA-binding domain of Kaposi's sarcoma-associated herpesvirus reveals structural conservation among gammaherpesvirus origin-binding proteins. J Gen Virol (2010) 0.94

Changes in skeletal muscle gene expression following clenbuterol administration. BMC Genomics (2006) 0.93

Epistasis: obstacle or advantage for mapping complex traits? PLoS One (2010) 0.93

Plants know where it hurts: root and shoot jasmonic acid induction elicit differential responses in Brassica oleracea. PLoS One (2013) 0.91

Analysis of viral cis elements conferring Kaposi's sarcoma-associated herpesvirus episome partitioning and maintenance. J Virol (2007) 0.91

Male-specific Fruitless isoforms have different regulatory roles conferred by distinct zinc finger DNA binding domains. BMC Genomics (2013) 0.90

Natural genetic variation in transcriptome reflects network structure inferred with major effect mutations: insulin/TOR and associated phenotypes in Drosophila melanogaster. BMC Genomics (2009) 0.89

Kaposi's sarcoma-associated herpesvirus microRNA single-nucleotide polymorphisms identified in clinical samples can affect microRNA processing, level of expression, and silencing activity. J Virol (2013) 0.88

Involvement of SSRP1 in latent replication of Kaposi's sarcoma-associated herpesvirus. J Virol (2009) 0.87

Epigenetic diversity of Kaposi's sarcoma-associated herpesvirus. Nucleic Acids Res (2013) 0.86

Identification of co-regulated transcripts affecting male body size in Drosophila. Genome Biol (2005) 0.85

Persistent human herpesvirus-6 infection in patients with an inherited form of the virus. J Med Virol (2013) 0.84

A flexible Bayesian method for detecting allelic imbalance in RNA-seq data. BMC Genomics (2014) 0.84

Comparison between NuGEN's WT-Ovation Pico and one-direct amplification systems. J Biomol Tech (2010) 0.84

Intersection tests for single marker QTL analysis can be more powerful than two marker QTL analysis. BMC Genet (2003) 0.84

Using alpha wisely: improving power to detect multiple QTL. Stat Appl Genet Mol Biol (2004) 0.83

Transcriptional network structure has little effect on the rate of regulatory evolution in yeast. Mol Biol Evol (2010) 0.82

Expression of defense genes in Drosophila evolves under a different selective regime from expression of other genes. Evolution (2010) 0.81

Partitioning transcript variation in Drosophila: abundance, isoforms, and alleles. G3 (Bethesda) (2011) 0.81

The SUMO conjugation pathway in Populus: genomic analysis, tissue-specific and inducible SUMOylation and in vitro de-SUMOylation. Planta (2010) 0.80

Evidence for an evolutionarily conserved interaction between cell wall biosynthesis and flowering in maize and sorghum. BMC Evol Biol (2002) 0.79

What the X has to do with it: differences in regulatory variability between the sexes in Drosophila simulans. Genome Biol Evol (2014) 0.77

Mapping density response in maize: a direct approach for testing genotype and treatment interactions. Genetics (2006) 0.77

High level expression of recombinant human antithrombin in the mammary gland of rabbits by adenoviral vectors infection. Anim Biotechnol (2012) 0.77

A systems biology approach identified different regulatory networks targeted by KSHV miR-K12-11 in B cells and endothelial cells. BMC Genomics (2014) 0.76