I am a molecular biologist specialising in genomics and transcriptomics of single cells and microscopic cell communities. My research directions include…
Determining “who is doing what” in very complex microbial communities. My current focus is on genes for elemental cycles and antibiotic resistance. The research builds on our recently published epicPCR methodology. The figure is adapted from Spencer, Tamminen et al (2016), released under CC BY 4.0. Read more here...
Determining “who is interacting with whom” in very complex microbial communities. I am currently focusing on physical interactions between microscopic eukaryotes and prokaryotes. This research also builds on epicPCR methodology. Read more here…
Increasing the sequence quality and throughput of current single cell genome sequencing pipelines. I am applying emulsion and hydrogel techniques to construct microscopic reaction compartments for a very large number of individual genome amplification reactions. I am also implementing screening workflows to target genome sequencing into defined genomic subpopulations. This builds on my emulsion work. More here...
News
February 16th 2021
Blaster available on CRAN! Finally a package for doing BLAST searches within your R session!
April 14th 2019
The life and works of J.S.Bach published online. This is my hobby project to gather and summarise all possible information about the great Baroque master!
November 7th 2018
Proteome evolution of Chlamydomonas reinhardtii under essential resource limitation. Out now in Nature Communications! Also check out our blog entry where we take a peek behind the scenes.
April 19th 2018
And another epicPCR paper out by Cairns et al! Tracking antibiotic resistance gene mobility in a mock community.
March 1st 2018
New epicPCR paper out by Hultman et al! This time targeting antibiotic resistance genes.
May 5th 2017
Tumor-infiltrating immune repertoires captured by single-cell barcoding in emulsion. Extremely high throughput single cell transcriptomics by Briggs et al out in bioRxiv.
October 21st 2016
Evaluating the mobility potential of antibiotic resistance genes in environmental resistomes without metagenomics. An exciting method by Katariina Pärnänen et al now out in Scientific Reports!
July 14th 2016
Mobile genes in the human microbiome are structured from global to individual scales. Amazing work by Ilana Brito et al fresh out in Nature!
April 29th 2016
“Every gene is everywhere but the environment selects” - our large-scale metagenome meta-analysis has been published in GBE.
January 19th 2016
Our epicPCR paper is out! Check it out here!
January 11th 2016
Just released a primer design package prider. This works on R and tries to make primer design from multiple sequence alignments easier.
November 10th 2015
My awesome colleague Sarah Spencer published this video detailing the workflow of epicPCR! https://www.youtube.com/watch?v=vgoI8U7lEzY