Gebruikersprofielen voor author:"Sreedharan Vipin T."
Vipin T. SreedharanPhD student at Memorial Sloan Kettering Cancer Center/ University of Tübingen Geverifieerd e-mailadres voor cbio.mskcc.org Geciteerd door 1284 |
[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 …
A spatial and temporal map of C. elegans gene expression
WC Spencer, G Zeller, JD Watson, SR Henz… - Genome …, 2011 - genome.cshlp.org
The C. elegans genome has been completely sequenced, and the developmental anatomy
of this model organism is described at single-cell resolution. Here we utilize strategies that
exploit this precisely defined architecture to link gene expression to cell type. We obtained …
of this model organism is described at single-cell resolution. Here we utilize strategies that
exploit this precisely defined architecture to link gene expression to cell type. We obtained …
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 …
Prediction of potent shRNAs with a sequential classification algorithm
We present SplashRNA, a sequential classifier to predict potent microRNA-based short
hairpin RNAs (shRNAs). Trained on published and novel data sets, SplashRNA outperforms
previous algorithms and reliably predicts the most efficient shRNAs for a given gene …
hairpin RNAs (shRNAs). Trained on published and novel data sets, SplashRNA outperforms
previous algorithms and reliably predicts the most efficient shRNAs for a given gene …
RNA‐Seq read alignments with PALMapper
Next‐generation sequencing technologies have revolutionized genome and transcriptome
sequencing. RNA‐Seq experiments are able to generate huge amounts of transcriptome
sequence reads at a fraction of the cost of Sanger sequencing. Reads produced by these …
sequencing. RNA‐Seq experiments are able to generate huge amounts of transcriptome
sequence reads at a fraction of the cost of Sanger sequencing. Reads produced by these …
The tumor profiler study: integrated, multi-omic, functional tumor profiling for clinical decision support
The application and integration of molecular profiling technologies create novel
opportunities for personalized medicine. Here, we introduce the Tumor Profiler Study, an
observational trial combining a prospective diagnostic approach to assess the relevance of …
opportunities for personalized medicine. Here, we introduce the Tumor Profiler Study, an
observational trial combining a prospective diagnostic approach to assess the relevance of …
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 …
[HTML][HTML] Cohesin rings devoid of Scc3 and Pds5 maintain their stable association with the DNA
I Kulemzina, MR Schumacher, V Verma, J Reiter… - PLoS …, 2012 - journals.plos.org
Cohesin is a protein complex that forms a ring around sister chromatids thus holding them
together. The ring is composed of three proteins: Smc1, Smc3 and Scc1. The roles of three
additional proteins that associate with the ring, Scc3, Pds5 and Wpl1, are not well …
together. The ring is composed of three proteins: Smc1, Smc3 and Scc1. The roles of three
additional proteins that associate with the ring, Scc3, Pds5 and Wpl1, are not well …
Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis
We present Oqtans, an open-source workbench for quantitative transcriptome analysis, that
is integrated in Galaxy. Its distinguishing features include customizable computational
workflows and a modular pipeline architecture that facilitates comparative assessment of …
is integrated in Galaxy. Its distinguishing features include customizable computational
workflows and a modular pipeline architecture that facilitates comparative assessment of …
[HTML][HTML] AspAlt: a tool for inter-database, inter-genomic and user-specific comparative analysis of alternative transcription and alternative splicing in 46 eukaryotes
A Bhasi, P Philip, VT Sreedharan, P Senapathy - Genomics, 2009 - Elsevier
We have developed AspAlt—a web-based comparative analytical platform for exploring the
variations in alternative transcription (AT) events and alternative splicing (AS) events in
eukaryotes. AspAlt provides integrated access to 2.1 million AT–AS annotations from 1 …
variations in alternative transcription (AT) events and alternative splicing (AS) events in
eukaryotes. AspAlt provides integrated access to 2.1 million AT–AS annotations from 1 …