Graduation ceremonies for Stella Pearless (MSc), Emily McIsaac (MSc), Georgia Breckell (PhD), and Arielle Sulit (PhD). Big year.


New article from Arielle on the immune response and treatment response in colorectal cancer patients (update from preprint below)


New article by Olin and collaborators Edo Kussell and Asher Steinberg quantifying recombination frequency in SARS-like coronaviruses


We've officially moved to our new building, a $130M glass and light-filled science building. Looking forward to seeing colleagues in the halls.


New article from Georgia on methylation and cell differentiation during growth (update from preprint below)


Our original 2020 SARS-CoV-2 sequencing method paper ("Midnight") moves past 100 citations (in only two years) and is the most cited paper *ever* in Biology Methods and Protocols


New paper published by Markéta on the evolution of gene regulation: Gene regulation in Escherichia coli is commonly selected for both high plasticity and low noise. Still more to come from this project...


New preprint by Arielle linking the microbiome content to colorectal cancer progression.


New preprint by Georgia highlighting the possibility of bacterial cell differentiation during growth!


New preprint by Markéta showing that the lacZ promoter is often selected to exhibit high transcriptional noise.


Congrats to Arielle, who passed her PhD exam with only minor emendations :) She'll be moving on to a postdoc at the University of Otago with Rachel Purcell


New paper published by William Pearman (long since left the lab) on the structure of isopod mitochondrial genomes


Bhargava and Olin (last minute replacement for Georgia) will talk at Virtual Nanopore Day Queenstown on detecting modifications of RNA (Bhargava) and DNA (Olin)


Congrats to Markéta, who passed her PhD examination with no emendations (something achieved by only 5% of all students)!!


Bhargava spoke at the 2021 FAOBMB meeting on detecting RNA modifications in bacteria using Oxford Nanopore sequencing.


New preprint from Georgia - Do You Want to Build a Genome? Benchmarking Hybrid Bacterial Genome Assembly Methods, in which we work towards ranking assembly methods using a number of different metrics.


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


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


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!


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.


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


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..


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!


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 


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.


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


(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!


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)


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


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 


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


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!


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


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


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


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.


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


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


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


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


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


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


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.


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.


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


Congrats to Bhargava for passing his PhD confirmation!


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.


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.


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


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...


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


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


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


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


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


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


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


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


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


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


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


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