About Me

Amber Rose Paulson, Ph.D. (she/her)

I am a white settler living and working on the traditional Territory of the lək̓ʷəŋən speaking peoples. I acknowledge and give thanks to the lessons and teachings I have received while living and working here in Victoria, BC. As a scientist, and in my work in the natural resource management sector of the BC Ministry of Environment and Climate Change Strategy I am committed to the Truth and Reconciliation Commission of Canada's Call to Action and upholding the United Nations Declaration on the Rights of Indigenous Peoples.

Current Research: epigenetic interference in SARS-CoV-2

My research explores the molecular evolution of epigenetic interference as an anti-host mechanism in RNA viruses. Leveraging advanced strategies in RNA-sequencing, integrative bioinformatics, and functional genetics, I hope my research will provide the missing link to fight back against emerging zoonotic diseases like SARS-CoV-2. 

Coverage of small RNA sequencing of SARS-CoV-2 isolate Wuhan-Hu-1 reference genome from Calu-3 cell 24 h post-infection (Wyler et al. 2021). Arrows indicate the locations of microRNAs of concern predicted in this study.

Notice to potential collaborators or industry partners - I am actively engaging in potential research opportunities in this space, so please reach out by email: Amber[dot]Rose[dot]Paulson[at]gmail[dot]com if you would like to explore potential collaborations related to pathogen-mediated epigenetic interference.

Please see the Mod-RNA pipeline video from the hackseqRNA - COVID19 Ultra-hackathon.

 

GitHub repository for Model_RNA

Past Research: transcriptome for pathogen and venom evolution

Tick microbiome:

Currently I am a voluntary postdoc with Dr. Rob Colautti at Queen's University, where I use high-throughput genetic sequencing to understand threat of emerging pathogens within blacklegged ticks - Ixodes scapularis, including Rickettsia buchneri,  Lyme disease borreliosis group Borrelia burgdorferi and RNA viruses.

I have developed an open-source R pipeline for analysis of 16S rRNA sequencing for bacteria associated with ticks with a manuscript in preparation (as of March 2022). 

In vivo transcriptome Yersinia

I was a Commonwealth Fellow for my PhD, complete with Dr. Mark Hurst at AgResearch Ltd. New Zealand., where I worked on transcriptome of entomopathogenic bacterium Yersinia entomophaga.

From Paulson et al. 2021 Circos plot of Y. entomophaga MH96 genome-wide transcriptional response to in vivo and in vitro conditions during early, middle, and late intrahemocoelic infection and lag, exponential and stationary growth, respectively. CPM, counts-per-million. Mean fold-change in log counts-per-million

See my CV for more details