Publications

CellNet – network biology applied to stem cell engineering

rna-seq

Somatic cell reprogramming, directed differentiation of pluripotent stem cells, and direct conversions between differentiated cell lineages represent powerful approaches to engineer cells for research and regenerative medicine. A team led by researchers at Boston Children’s Hospital have developed CellNet, a ...

Read More »

High-Resolution Transcriptome Analysis with Long-Read RNA Sequencing

rna-seq

RNA sequencing (RNA-seq) enables characterization and quantification of individual transcriptomes as well as detection of patterns of allelic expression and alternative splicing. Current RNA-seq protocols depend on high-throughput short-read sequencing of cDNA. However, as ongoing advances are rapidly yielding increasing ...

Read More »

Transcription Start Site Associated RNAs (TSSaRNAs) Are Ubiquitous in All Domains of Life

rna-seq

A plethora of non-coding RNAs has been discovered using high-resolution transcriptomics tools, indicating that transcriptional and post-transcriptional regulation is much more complex than previously appreciated. Small RNAs associated with transcription start sites of annotated coding regions (TSSaRNAs) are pervasive in ...

Read More »

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 ...

Read More »

Next-generation RNA Sequencing of Archival Formalin-fixed Paraffin-embedded tissue

rna-seq

Molecular profiling of individual cancers is key to personalised medicine. While sequencing technologies have required stringent sample collection and handling, recent technical advances offer sequencing from tissues collected in routine practice and tissues already stored in archives. In this paper, ...

Read More »

RNA-Seq of the Nucleolus Reveals Abundant SNORD44-Derived Small RNAs

rna-seq

Small non-coding RNAs represent RNA species that are not translated to proteins, but which have diverse and broad functional activities in physiological and pathophysiological states. The knowledge of these small RNAs is rapidly expanding in part through the use of ...

Read More »