Tag Archives: RNA-Seq

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piPipes – a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing

piPipes – a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing

PIWI-interacting RNAs (piRNAs), 23-36 nt small silencing RNAs, repress transposon expression in the metazoan germ line, thereby protecting the genome. Although high-throughput sequencing has made it possible to examine the genome and transcriptome at unprecedented resolution, extracting useful information from ...

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Enabling large-scale next-generation sequence assembly with Blacklight

Enabling large-scale next-generation sequence assembly with Blacklight

A variety of extremely challenging biological sequence analyses were conducted on the XSEDE large shared memory resource Blacklight, using current bioinformatics tools and encompassing a wide range of scientific applications. These include genomic sequence assembly, very large metagenomic sequence assembly, ...

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Post-doc Postions Available – Texas State University

Post-doc Postions Available – Texas State University

One or two postdoctoral positions are available immediately in Oncinfo Lab, Department of Computer Science at Texas State University. Position description The successful candidates will contribute to development and application of cutting edge computational methods to analyze RNA-seq and other ...

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Meet the Winner of Appistry’s Pipeline Challenge

Meet the Winner of Appistry’s Pipeline Challenge

Today Appistry announced the winner of its inaugural Pipeline Challenge. The winner is a project team led by Dr. Benjamin Darbro, director of the Shivanand R. Patil Cytogenetics and Molecular Laboratory at the University of Iowa Hospital and Clinics. Dr. Darbro won ...

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Leveraging the complementary nature of RNA-Seq and shotgun proteomics data

Leveraging the complementary nature of RNA-Seq and shotgun proteomics data

RNA sequencing (RNA-Seq) and mass spectrometry-based shotgun proteomics are powerful high-throughput technologies for identifying and quantifying RNA transcripts and proteins respectively. With the increasing affordability of these technologies, many projects have started to apply both to the same samples to ...

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RNA-Seq and RNA Structure Prediction

RNA-Seq and RNA Structure Prediction

by Xiaole Shirley Liu RNA-seq Experiments Analysis: read mapping, expression index, isoform inference, differential expression RNA structure prediction Covariance model Base-pair maximization Free energy method

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