Dr Michelle Allen

Michelle is an experienced bioinformatician managing large-scale genomic and metagenomic datasets, with a strong biological background in molecular biology, ‘omic technologies and environmental research.

Professional Experience

2006 - present     Postdoctoral Research Associate, Cavicchioli Lab, UNSW
2003 (3 mths)       NASA Planetary Biology Internship
2001 - 2006         PhD student, UNSW
2000 - 2001         Lab manager and Research Assistant, Dalton Lab, UNSW

Research Contribution

My role in the Cavicchioli lab is to research the fascinating cold-adapted organisms and communities living in Antarctic lakes and waters, predominantly using bioinformatics.

The Cavicchioli lab has been an early adopter of ‘omic technologies, and since 2006 our genomic data has grown from a single genome of a methanogenic archaeon (Methanococcoides burtonii, isolated from Ace Lake, Antarctica), to a massive 380+ metagenomes (Sanger, 454, Illumina and Nanopore data; over 4 TB of qc-filtered reads) from an array of Antarctic lakes and waters.
I manage and analyze these datasets to extract novel insight into the taxonomic diversity, adaptation, ecology and nutrient cycling of the various lakes.

Highlights include discovering novel organisms and symbioses, tracking gene exchange (including HIR) and viral interactions, interrogating our seasonal time-series data, and integrating our metagenome results with experimental data to better understand these unique communities.

I enjoy collaborating with others and have also been involved in supervising/mentoring a number of Honours, Masters and PhD students.

My Expertise

Bioinformatics; Next-Generation Sequencing, QC and assembly; Metagenome-assembled genome (MAG) binning; Annotation of genomes and MAGs; Phylogenetics; Diversity, correlation and multivariate analyses; Data visualization; Integration of metagenomic data with experimental data (eg proteomics)

Molecular biology; Microbial ecology; Culturing diverse organisms including cyanobacteria, archaea and heterotrophic bacteria; Isolation and characterization of novel Haloarchaea; Archaeal biology; Analysis of biofilm formation mutants using in vitro reactors, time-lapse microscopy and high-throughput screening; Confocal, FISH and Electron Microscopy

Extraction, purification, identification and analysis of lipid biomarkers using GC-MS; Stromatolite and microbial mat communities; Astrobiology