Tag Archives: Johns Hopkins University

Chemical probing methods are crucial to our understanding of the structure and function of RNA molecules. The majority of chemical methods used to probe RNA structure report on Watson-Crick pairing, but tertiary structure parameters such as solvent...

Gene expression profiling can uncover biologic mechanisms underlying disease and is important in drug development. RNA sequencing (RNA-seq) is routinely used to assess gene expression, but costs...

A research assistant job in statistical analysis (including algorithm design and evaluation) of large-scale single-cell and bulk RNA-seq data...

useR! International R User 2017 Conference – July 7, 2017 Kai Kammers  – Johns Hopkins University School of Medicine

Public sequencing data archives are growing by petabases — millions of billions of DNA letters — per year. But for typical researchers, using these data requires huge downloads and laborious re-analysis. Most researchers aren’t equipped for this, so valuable data ...

Gene annotations, such as those in GENCODE, are derived primarily from alignments of spliced cDNA sequences and protein sequences. The impact of RNA-seq data on annotation has been confined to major projects like ENCODE and Illumina Body Map 2.0. Researchers ...

Differential expression analysis of RNA sequencing (RNA-seq) data typically relies on reconstructing transcripts or counting reads that overlap known gene structures. Researchers at Johns Hopkins University previously introduced an intermediate statistical approach called differentially expressed region (DER) finder that seeks ...

Conventional high-throughput technologies for mapping regulatory element activities such as ChIP-seq, DNase-seq and FAIRE-seq cannot analyze samples with small number of cells. The recently developed ATAC-seq allows regulome mapping in small-cell-number samples, but its signal in single cell or samples ...

Next-generation sequencing of cellular RNA (RNA-seq) is rapidly becoming the cornerstone of transcriptomic analysis. However, sequencing errors in the already short RNA-seq reads complicate bioinformatics analyses, in particular alignment and assembly. Error correction methods have been highly effective for whole-genome ...

from Gizmodo by Jennifer Ouellette Last year’s hugely popular “ice bucket challenge” saw celebrities pouring buckets of ice water over their heads to help fight Lou Gehrig’s Disease (ALS). Skeptics dismissed it as mere “slacktivism,” but researchers told us that ...