Published in PLoS Genet on January 16, 2014
Transcriptional control of HIV latency: cellular signaling pathways, epigenetics, happenstance and the hope for a cure. Virology (2014) 1.45
Comprehensive analysis of RNA-protein interactions by high-throughput sequencing-RNA affinity profiling. Nat Methods (2014) 1.27
New Technologies Provide Quantum Changes in the Scale, Speed, and Success of SELEX Methods and Aptamer Characterization. Mol Ther Nucleic Acids (2014) 1.21
Negative elongation factor is required for the maintenance of proviral latency but does not induce promoter-proximal pausing of RNA polymerase II on the HIV long terminal repeat. Mol Cell Biol (2014) 1.03
Integrator complex regulates NELF-mediated RNA polymerase II pause/release and processivity at coding genes. Nat Commun (2014) 1.01
A Two-Way Street: Regulatory Interplay between RNA Polymerase and Nascent RNA Structure. Trends Biochem Sci (2016) 0.86
RNA polymerase-induced remodelling of NusA produces a pause enhancement complex. Nucleic Acids Res (2015) 0.86
Regulatory feedback from nascent RNA to chromatin and transcription. Nat Rev Mol Cell Biol (2017) 0.80
High-throughput binding characterization of RNA aptamer selections using a microplate-based multiplex microcolumn device. Anal Bioanal Chem (2014) 0.80
RNA polymerase II pausing as a context-dependent reader of the genome. Biochem Cell Biol (2015) 0.77
Architecture and RNA binding of the human negative elongation factor. Elife (2016) 0.77
Quantitative assessment of RNA-protein interactions with high-throughput sequencing-RNA affinity profiling. Nat Protoc (2015) 0.76
Highly Multiplexed RNA Aptamer Selection using a Microplate-based Microcolumn Device. Sci Rep (2016) 0.75
SIRT7 Is an RNA-Activated Protein Lysine Deacylase. ACS Chem Biol (2016) 0.75
SERPINB2 is regulated by dynamic interactions with pause-release proteins and enhancer RNAs. Mol Immunol (2017) 0.75
Transcriptional response to stress is pre-wired by promoter and enhancer architecture. Nat Commun (2017) 0.75
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol (2009) 235.12
Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res (2003) 77.89
The genome sequence of Drosophila melanogaster. Science (2000) 74.32
Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A (1992) 61.33
Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol (1994) 37.96
Sequence logos: a new way to display consensus sequences. Nucleic Acids Res (1990) 36.74
Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science (2008) 16.48
The UCSC Genome Browser database: update 2011. Nucleic Acids Res (2010) 16.24
MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res (2006) 15.32
The Jpred 3 secondary structure prediction server. Nucleic Acids Res (2008) 13.32
c-Myc regulates transcriptional pause release. Cell (2010) 11.64
A novel CDK9-associated C-type cyclin interacts directly with HIV-1 Tat and mediates its high-affinity, loop-specific binding to TAR RNA. Cell (1998) 10.14
RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nat Genet (2007) 9.56
The kink-turn: a new RNA secondary structure motif. EMBO J (2001) 8.58
Breaking barriers to transcription elongation. Nat Rev Mol Cell Biol (2006) 8.18
DSIF, a novel transcription elongation factor that regulates RNA polymerase II processivity, is composed of human Spt4 and Spt5 homologs. Genes Dev (1998) 6.96
HIV-1 tat trans-activation requires the loop sequence within tar. Nature (1988) 6.87
Control of RNA polymerase II elongation potential by a novel carboxyl-terminal domain kinase. J Biol Chem (1996) 6.78
The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression. FEBS J (2005) 6.72
NELF, a multisubunit complex containing RD, cooperates with DSIF to repress RNA polymerase II elongation. Cell (1999) 6.34
Application of multiple sequence alignment profiles to improve protein secondary structure prediction. Proteins (2000) 6.22
Overcoming expression and purification problems of RhoGDI using a family of "parallel" expression vectors. Protein Expr Purif (1999) 5.90
Purification of P-TEFb, a transcription factor required for the transition into productive elongation. J Biol Chem (1995) 5.31
Searching for patterns in genomic data. Trends Genet (1997) 5.28
Human immunodeficiency virus 1 tat protein binds trans-activation-responsive region (TAR) RNA in vitro. Proc Natl Acad Sci U S A (1989) 5.03
Defining mechanisms that regulate RNA polymerase II transcription in vivo. Nature (2009) 4.31
Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation. Cell (2010) 4.28
Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila. Science (2009) 4.13
P-TEFb kinase recruitment and function at heat shock loci. Genes Dev (2000) 4.07
HIV-1 tat protein stimulates transcription by binding to a U-rich bulge in the stem of the TAR RNA structure. EMBO J (1990) 3.92
NELF-mediated stalling of Pol II can enhance gene expression by blocking promoter-proximal nucleosome assembly. Genes Dev (2008) 3.69
Transcription factor and polymerase recruitment, modification, and movement on dhsp70 in vivo in the minutes following heat shock. Mol Cell Biol (2003) 3.65
Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells. Genes Dev (2011) 3.55
NELF and GAGA factor are linked to promoter-proximal pausing at many genes in Drosophila. Mol Cell Biol (2008) 3.11
Evidence that negative elongation factor represses transcription elongation through binding to a DRB sensitivity-inducing factor/RNA polymerase II complex and RNA. Mol Cell Biol (2002) 2.59
Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. Science (2013) 2.51
Dynamics of human immunodeficiency virus transcription: P-TEFb phosphorylates RD and dissociates negative effectors from the transactivation response element. Mol Cell Biol (2004) 2.49
NELF interacts with CBC and participates in 3' end processing of replication-dependent histone mRNAs. Mol Cell (2007) 2.24
Human transcription elongation factor NELF: identification of novel subunits and reconstitution of the functionally active complex. Mol Cell Biol (2003) 2.21
The control of HIV transcription: keeping RNA polymerase II on track. Cell Host Microbe (2011) 2.05
SR proteins collaborate with 7SK and promoter-associated nascent RNA to release paused polymerase. Cell (2013) 1.97
Defining the status of RNA polymerase at promoters. Cell Rep (2012) 1.91
Transcriptional and posttranscriptional regulation of HIV-1 gene expression. Cold Spring Harb Perspect Med (2012) 1.88
P-TEFb is critical for the maturation of RNA polymerase II into productive elongation in vivo. Mol Cell Biol (2007) 1.81
Molecular basis of RNA recognition by the embryonic polarity determinant MEX-5. J Biol Chem (2007) 1.61
Interactions between DSIF (DRB sensitivity inducing factor), NELF (negative elongation factor), and the Drosophila RNA polymerase II transcription elongation complex. Proc Natl Acad Sci U S A (2010) 1.55
Quantitative approaches to monitor protein-nucleic acid interactions using fluorescent probes. RNA (2010) 1.40
The importance of G.A hydrogen bonding in the metal ion- and protein-induced folding of a kink turn RNA. J Mol Biol (2008) 1.21
RNA recognition by the embryonic cell fate determinant and germline totipotency factor MEX-3. Proc Natl Acad Sci U S A (2009) 1.11
Structural studies on the RNA-recognition motif of NELF E, a cellular negative transcription elongation factor involved in the regulation of HIV transcription. Biochem J (2006) 0.93
Screening of lambda library for differentially expressed genes using in vitro transcripts. Anal Biochem (1985) 0.91
Multiplexed microcolumn-based process for efficient selection of RNA aptamers. Anal Chem (2013) 0.89
RAPID-SELEX for RNA aptamers. PLoS One (2013) 0.88
NELF-E RRM undergoes major structural changes in flexible protein regions on target RNA binding. Biochemistry (2008) 0.83
End-labeling oligonucleotides with chemical tags after synthesis. Methods Mol Biol (2012) 0.82
The Hmr and Lhr hybrid incompatibility genes suppress a broad range of heterochromatic repeats. PLoS Genet (2014) 1.00
RAPID-SELEX for RNA aptamers. PLoS One (2013) 0.88
GAGA factor maintains nucleosome-free regions and has a role in RNA polymerase II recruitment to promoters. PLoS Genet (2015) 0.86
Targeted H3R26 deimination specifically facilitates estrogen receptor binding by modifying nucleosome structure. PLoS Genet (2014) 0.78
Discovering aptamers by cell-SELEX against human soluble growth factors ectopically expressed on yeast cell surface. PLoS One (2014) 0.75