Tag Archives: genomics

Considerations for RNA-Seq Analysis of Circadian Rhythms

Circadian rhythms are daily endogenous oscillations of behavior, metabolism, and physiology. At a molecular level, these oscillations are generated by transcriptional-translational feedback loops composed of core clock genes. In turn, core clock genes drive the rhythmic accumulation of downstream outputs-termed ...

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Making Single-Cell Biology Work

rna-seq

New Collaboration Between EMBL-EBI, the Wellcome Trust Sanger Institute and Fluidigm Keeps Research and Technology on the Cutting-Edge of Single-Cell Genomics December 17, 2014 06:24 AM Eastern Standard Time SOUTH SAN FRANCISCO, Calif. & HINXTON, U.K.–(BUSINESS WIRE)–A formal collaboration was ...

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Roadmap to the epitranscriptome

The “RNA world” is not at all hypothetical but rather the biological world we live in (1). For RNA to function within a modern cellular milieu of proteins and DNA, numerous chemical modifications coevolved that help sculpt its interactions (2). ...

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BioVLAB-MMIA-NGS – MicroRNA-mRNA Integrated Analysis using High Throughput Sequencing Data

rna-seq

It is now well established that microRNAs (miRNAs) play a critical role in regulating gene expression in a sequence specific manner and genome-wide efforts are underway to predict known and novel miRNA targets. However, the integrated miRNA-mRNA analysis remains a ...

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Enabling large-scale next-generation sequence assembly with Blacklight

rna-seq

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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The evolution of black widow venom

Black widow venom contains α-latrotoxin, infamous for causing intense pain. Combining 33kb of Latrodectus hesperus genomic DNA with RNA-Seq, we characterized the α-latrotoxin gene and discovered a paralog, 4.5kb downstream. Both paralogs exhibit venom gland specific transcription, and may be ...

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subSeq – Determining appropriate sequencing depth through efficient read subsampling

rna-seq

Next-generation sequencing experiments, such as RNA-Seq, play an increasingly important role in biological research. One complication is that the power and accuracy of such experiments depends substantially on the number of reads sequenced, so it is important and challenging to ...

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SUPPA – a super-fast pipeline for alternative splicing analysis from RNA-Seq

rna-seq

High-throughput RNA sequencing allows genome-wide analyses of pre-mRNA splicing across multiple conditions. However, the increasing number of available datasets represents a major challenge in terms of time and storage required for analyses. Now, a team led by researchers at the ...

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Featured RNA-Seq Job – Informatics Institute Next-Generation Sequencing (NGS) Analyst/Consultant

rna-seq

University of Minnesota, Twin Cities Duties/Responsibilities: The University of Minnesota Informatics Institute (UMII) and University of Minnesota Genomics Center (UMGC) seek a skilled, Ph.D.-level analyst to serve as both internal NGS analyst and client-facing NGS consultant. The UMGC is the ...

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