[HTML][HTML] Determination and inference of eukaryotic transcription factor sequence specificity
MT Weirauch, A Yang, M Albu, AG Cote… - Cell, 2014 - Elsevier
Transcription factor (TF) DNA sequence preferences direct their regulatory activity, but are
currently known for only∼ 1% of eukaryotic TFs. Broadly sampling DNA-binding domain
(DBD) types from multiple eukaryotic clades, we determined DNA sequence preferences …
currently known for only∼ 1% of eukaryotic TFs. Broadly sampling DNA-binding domain
(DBD) types from multiple eukaryotic clades, we determined DNA sequence preferences …
[HTML][HTML] Multiple reference genomes and transcriptomes for Arabidopsis thaliana
Genetic differences between Arabidopsis thaliana accessions underlie the plant's extensive
phenotypic variation, and until now these have been interpreted largely in the context of the
annotated reference accession Col-0. Here we report the sequencing, assembly and …
phenotypic variation, and until now these have been interpreted largely in the context of the
annotated reference accession Col-0. Here we report the sequencing, assembly and …
RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer
The translational control of oncoprotein expression is implicated in many cancers. Here we
report an eIF4A RNA helicase-dependent mechanism of translational control that contributes
to oncogenesis and underlies the anticancer effects of silvestrol and related compounds. For …
report an eIF4A RNA helicase-dependent mechanism of translational control that contributes
to oncogenesis and underlies the anticancer effects of silvestrol and related compounds. For …
DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation
Epigenome modulation potentially provides a mechanism for organisms to adapt, within and
between generations. However, neither the extent to which this occurs, nor the mechanisms
involved are known. Here we investigate DNA methylation variation in Swedish Arabidopsis …
between generations. However, neither the extent to which this occurs, nor the mechanisms
involved are known. Here we investigate DNA methylation variation in Swedish Arabidopsis …
Nonsense-mediated decay of alternative precursor mRNA splicing variants is a major determinant of the Arabidopsis steady state transcriptome
G Drechsel, A Kahles, AK Kesarwani, E Stauffer… - The Plant …, 2013 - Am Soc Plant Biol
The nonsense-mediated decay (NMD) surveillance pathway can recognize erroneous
transcripts and physiological mRNAs, such as precursor mRNA alternative splicing (AS)
variants. Currently, information on the global extent of coupled AS and NMD remains scarce …
transcripts and physiological mRNAs, such as precursor mRNA alternative splicing (AS)
variants. Currently, information on the global extent of coupled AS and NMD remains scarce …
Determinants of robustness in spindle assembly checkpoint signalling
S Heinrich, EM Geissen, J Kamenz, S Trautmann… - Nature cell …, 2013 - nature.com
The spindle assembly checkpoint is a conserved signalling pathway that protects genome
integrity. Given its central importance, this checkpoint should withstand stochastic
fluctuations and environmental perturbations, but the extent of and mechanisms underlying …
integrity. Given its central importance, this checkpoint should withstand stochastic
fluctuations and environmental perturbations, but the extent of and mechanisms underlying …
RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints
Motivation Deep sequencing based ribosome footprint profiling can provide novel insights
into the regulatory mechanisms of protein translation. However, the observed ribosome
profile is fundamentally confounded by transcriptional activity. In order to decipher principles …
into the regulatory mechanisms of protein translation. However, the observed ribosome
profile is fundamentally confounded by transcriptional activity. In order to decipher principles …
MITIE: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples
Motivation: High-throughput sequencing of mRNA (RNA-Seq) has led to tremendous
improvements in the detection of expressed genes and reconstruction of RNA transcripts.
However, the extensive dynamic range of gene expression, technical limitations and biases …
improvements in the detection of expressed genes and reconstruction of RNA transcripts.
However, the extensive dynamic range of gene expression, technical limitations and biases …
Accurate detection of differential RNA processing
Deep transcriptome sequencing (RNA-Seq) has become a vital tool for studying the state of
cells in the context of varying environments, genotypes and other factors. RNA-Seq profiling
data enable identification of novel isoforms, quantification of known isoforms and detection …
cells in the context of varying environments, genotypes and other factors. RNA-Seq profiling
data enable identification of novel isoforms, quantification of known isoforms and detection …
Statistical tests for detecting differential RNA-transcript expression from read counts
As a fruit of the current revolution in sequencing technology, transcriptomes can now be
analyzed at an unprecedented level of detail. These advances have been exploited for
detecting differential expressed genes across biological samples and for quantifying the …
analyzed at an unprecedented level of detail. These advances have been exploited for
detecting differential expressed genes across biological samples and for quantifying the …