Blackburn, Jessica

Research Activities

Our group focuses on identifying novel mechanisms and drugable targets that contribute to the progression of several childhood cancers, such as T-cell acute lymphoblastic leukemia (T-ALL) and Diffuse Intrinsic Pontine Glioma (DIPG). We utilize a multitude of genetic tools and molecular approaches to study these diseases such as, CRISPR knock-out/in, single-cell RNASeq, long-read nanopore sequencing, etc. Our current research relies strongly on the zebrafish model to elucidate functions of certain onco-genes and tumor progressors. In addition, we are interested in developing novel technologies that can be applied by other zebrafish researchers to move the field forward.

Cluster Based Projects

Nanopore Whole Genome Sequencing

Current and near future research activities include (but are not limited to) using long-read, nanopore sequencing to re-assemble the Danio rerio genome in an effort to increase accuracy, increase mapping of previously unmapped regions, and fix inaccurately mapped locations. Newly assembled genome will be compared to current GRCz11 assembly across transposon and repeat regions (centromeric and telomeric), novel mapping of biologically relevant genes and enhancer elements in addition to other genetic features.

Additionally, we may be interested in sequencing two Danio rerio strains to assess at divergence and variation between the two.

Personnel:

Dr. Jessica Blackburn, PI

Dr. Yelena Chernyavskaya, Scientist II 

Dr. Jeramiah Smith

Computational/Software:

Canu, Pilon, Mummer, LASTZ (We will be doing alignments and making genomic assemblies)

Collaborators:

All personnel listed are UK associated collaborators.