News

Rachael Workman presented her recent work using PacBio’s RNA sequencing pipeline (IsoSeq) for de novo transcriptome sequencing of the ruby-throated hummingbird in Baltimore on June 8th. Here (Workman_isoseq_PUGM2) is a link to her slides. Great job Rachael!

Stephanie Hao presented her recent work on using nanopore sequencing for infectious disease diagnosis and characterization at the Oxford Nanopore user group meeting (London Calling) in London on May 26th. Here (LondonCalling16_SHao_final_v2_website) is a link to her slides. Great job Stephanie!

Alexis was highlighted for our paper on structural variation detection with nanopores (http://www.tandfonline.com/doi/full/10.1080/15384047.2016.1139236). ASHG link here: http://www.ashg.org/education/PaperSpotlight_Norris.shtml

Let’s all congratulate Rachael – she won the rookie of the year award given by the Whiting School of Engineering for her awesome work over the past year in lab.

https://www.genomeweb.com/sequencing-technology/nanopore-sequencing-identifies-methylation-marks-help-new-statistical-methods

We just put up our preprint (w/ Jared Simpson at OICR) of our work to use the MinION to call methylation – see here: http://biorxiv.org/content/biorxiv/early/2016/04/04/047142

We’re submitting it for peer review soon, but all the analysis code is here (https://github.com/jts/methylation-analysis)

Our grant, headed by Ken Welch (UToronto) was awarded from the Human Frontier Science Program: “Optimization of metabolic flux in the hummingbird: from enzymes to ecology”.  Our part in the grant involves transcriptomic and epigenetic characterization of the hummingbird to understand its incredible metabolism, using diverse sequencing tools including PacBio IsoSeq and chromatin/methylation profiling. The interdisciplinary team includes: Dr. Welch (UToronto) has expertise in hummingbird ecology and metabolic physiology, Dr. Timp (JHU) is an expert in genomic and computational approaches, Dr. Wong (JHU) brings experience in biochemistry and the molecular biology of metabolic enzymes, and Dr. Valle (Center for Cooperative Research in Biosciences) is an expert in biophysics and structural biology.

We’re currently using resources and help provided by PacBio to help us with a first de novo transcriptome of the hummingbird liver to understand the differences in its genes.

At Cancer Biology and Therapy (http://www.tandfonline.com/loi/kcbt20) – congrats to Yunfan and Rachael for all their hard work, as well as our collaborators Jim and Alexis.

Discussed as part of a larger survey trying to examine methods to profile DNA methylation: http://www.nature.com/nmeth/journal/v13/n2/full/nmeth.3736.html