News


2021-09-29

New preprint with ex-collaborator William Pearman (now at the University of Otago: Long read sequencing reveals atypical mitochondrial genome structure in a New Zealand marine isopod

2021-09-01

Oxford Nanopore is now offering the primer set we developed here as a full kit, description of the method here (by ONT).

2021-08-01

Markéta's paper on the efficiency of the self-cleaving ribozyme RiboJ is now published in MicrobiologyOpen. Her first first-author publication in the lab!

2021-07-19

New preprint: Gene regulation is commonly selected for high plasticity and low noise. We show that in E. coli, selection acts strongly to increase plasticity - the difference in expression level of a gene in one environment versus another. A huge effort by Markéta.

2021-05-01

Our paper (with collaborator Jemma Geophegan and others from ESR and the University of Auckland is now published in Emerging and Infectious Diseases.

2021-05-01

The paper on SARS-CoV-2 spread co-ordinated Aine O-Toole and others (in which we played a small part collecting SARS-CoV-2 sequence data) is now published in Wellcome Open Research..

2021-03-20

We've posted a new pre-print in which we explore whether a self-splicing ribozyme (RiboJ) behaves robustly across different cis- and trans- genetic contexts. Congrats to Markéta, who did the vast majority of work on the project!

2021-02-06

Congratulations to Georgia, on her publication with collaborator Sara Burgess - Characterisation of AmpC and extended-spectrum beta-lactamase producing E. coli from New Zealand dairy farms

2021-01-18

We have a two-year fully funded MSc Scholarship (with stipend) available, starting as soon as possible. The project will examine interactions between bacteria and whether these interactions change if bacteria have different environmental histories (and memories of those different histories). Please email if this sounds interesting! There is some flexibility in the direction that the project takes.

2021-01-15

Áine O'Toole has posted on virological.org about the spread of the SARS-CoV-2 B.1.1.7 lineages. We contributed a small amount of sequence data for this study.

2020-12-04

(Ex lab-associate) William Pearman's paper Concordant geographic and genetic structure revealed by genotyping‐by‐sequencing in a New Zealand marine isopod (modified title from the pre-print here) is published in Ecology and Evolution!

2020-11-16

New Marsden grant! Predicting evolution: Quantifying the emergence of antibiotic resistance in diverse environmental strains of E. coli, $300K. Nikki Freed (PI) and Olin Silander (AI)

2020-11-05

Congrats to Julia White, who was awarded one of the $3K SNCS Summer Scholarships (again!)!

2020-11-04

New preprint out: The power and limitations of genomics to track COVID-19 outbreaks: a case study from New Zealand. We played a small part in getting the sequencing data for this study, which was led by Jemma Geoghegan

2020-11-03

The primer pools we developed for SARS-CoV-2 genome sequencing (publication here and protocol here) are now being offered by IDT:

Product Name: SARS-Cov2-Midnight-1200, 500rxn

Product number: 10007184

2020-10-01

Andrea's manuscript on profiling bacterial strains and antimicrobial resistance loci using CRISPR-Cas9 enrichment and long read sequencing (Bac-PULCE) is now posted as a preprint on bioRxiv!

2020-09-17

Georgia's Microbial Resource Announcements paper, Complete Genome Sequences of 47 Environmental Isolates of Escherichia coli is now published! Congrats!

2020-09-09

The new release of the UCSC COVID-19 genome browser now includes a track for our 1200bp rapid primers (published here)

2020-08-25

Congratulations to Georgia Breckell and Markéta Vlková, who were both awarded Sir Neil Waters Scholarships

2020-08-14

Olin, Nikki, and Markéta completed genome sequencing for 19 new SARS-CoV-2 genomes (in ~ 8 hours for each set of samples) to establish linkages for the new SARS-CoV-2 outbreak in Auckland. News story here. Link to some Twitter discussions and here (with article) and here. This was very exciting work and provided the first genomic evidence that this was a single cluster.

2020-07-23

Olin and Nikki Freed were interviewed on RNZ Nights about new genome sequencing methods for SARS-CoV-2

2020-07-18

Our paper on a new rapid method for SARS-CoV-2 genome sequencing was published in Biology Methods and Protocols

2020-06-02

We've posted a preprint detailing and benchmarking our new (improved) method for SARS-CoV-2 genome sequencing.

2020-05-30

One day later William Pearman has left the building to start his PhD at Otago :( Good luck!

2020-05-29

William Pearman's article on using long reads vs. short reads for metagenomics is published!

2020-05-23

We've posted a new protocol for SARS-CoV-2 genome sequencing on protocols.io

2020-04-15

We've received some funding from the Health Research Council and Ministry of Health to develop methods for saving time and money for SARS-CoV-2 diagnosis and genome sequencing.

2020-03-01

We've posted the preprint about the work we've been doing on the population structure of the NZ endemic marine isopod Isocladus armatus. We used DaRT seq (a genotypting-by-sequencing method) to analyse population structure across New Zealand.

2020-02-01

Welcome to Stella Pearless, a new MSc who will work on characterising phenotype switching in natural isolates of E. coli!

2019-12-12

Congrats to Bhargava for passing his PhD confirmation!

2019-12-04

Sara Burgess from Massey Palmerston North is up for the week to improve her Oxford Nanopore sequencing technique (PhCHCl3 and circulomics) and get in some data analysis. Hopefully we won't disappoint her with mediocre run yields.

2019-11-25

Markéta (Effects of Single SNPS on Gene Expression) and Georgia (So you wanna build a genome) presented talks at the New Zealand Microbiological Society 2019 meeting, while Georgia, Andrea (Rapid CRISPR-based Identification of Microorganisms - a Proof of Concept), Bhargava (Full length cDNA sequencing to study transcriptional regulation in bacteria), and Alyssa (Metagenomic analysis of cow faecal samples) presented posters.

2019-11-11

We've started a collaboration with Fonterra to profile the community of their membrane bioreactors using metagenomic and 16S analyses. More faeces!

2019-11

A brilliant month of rejections: Andrea (PhD scholarship application rejected); Olin (AMRF grant rejected); and fellow PI Nikki Freed (2nd round Marsden grant rejected). Moving on...

2019-10-21

Congrats to William and Bhargava for their awards at the annual SNCS postgraduate conference (1st place talk and 2nd place poster presentation, respectively).

2019-10-07

Congrats to Julia White, who was awarded one of the $6K SNCS Summer Scholarships!

2019-10-01

Welcome to Julia White, who is joining the lab as an undergraduate volunteer.

2019-09-06

Markéta (pdf here) and Georgia (pdf here) presented posters at the Queenstown Molecular Biology Meeting.

2019-09-05

Olin gave one of the monthly seminars organised as part of the Evolution Research @ Auckland Network.

2019-08-27

Olin gave a public lecture on human genomics as part of the Fascination Science series at Massey.

2019-08-01

Welcome to Jamie le Roux, who is joining the lab as a Research intern.

2019-08-01

Welcome to Andrea Sajuthi, who is joining the lab as a new PhD student.

2019-07-24

Congratulations to Georgia Breckell, who was awarded a travel scholarship to the Queenstown Molecular Biology Meeting.

2019-07-19

Welcome to Katie Littlewood, who is joining the lab as an undergraduate intern.

2019-06-20

We were awarded $10K in seed funding from the Digital Life Institute for proof-of-concept design and production of synthetic bacteriophage.

2019-05-23

Congratulations to Markéta Vlkova for being selected for an oral presentation at the Microbial Population Biology Gordon Research Seminar.