Dr Michelle Allen
Research Associate

Dr Michelle Allen

Science
School of Biotech & Biomolecular Science

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

 

Location
School of Biotechnology and Biomolecular Sciences Level 4 West, Biosciences South Building (E26)
  • Book Chapters | 2016
    Burns B; Goh F; Allen M; Shi R; Neilan B, 2016, 'Extant Analogues of the Microbial Origins of Life', in Geomicrobiology, Taylor & Francis, pp. 237 - 254, http://dx.doi.org/10.1201/b10193-9
  • Journal articles | 2022
    Williams TJ; Allen MA; Panwar P; Cavicchioli R, 2022, 'Into the darkness: the ecologies of novel ‘microbial dark matter’ phyla in an Antarctic lake', Environmental Microbiology, vol. 24, pp. 2576 - 2603, http://dx.doi.org/10.1111/1462-2920.16026
    Journal articles | 2021
    Nayfach S; Roux S; Seshadri R; Udwary D; Varghese N; Schulz F; Wu D; Paez-Espino D; Chen IM; Huntemann M; Palaniappan K; Ladau J; Mukherjee S; Reddy TBK; Nielsen T; Kirton E; Faria JP; Edirisinghe JN; Henry CS; Jungbluth SP; Chivian D; Dehal P; Wood-Charlson EM; Arkin AP; Tringe SG; Visel A; Abreu H; Acinas SG; Allen E; Allen MA; Alteio LV; Andersen G; Anesio AM; Attwood G; Avila-Magaña V; Badis Y; Bailey J; Baker B; Baldrian P; Barton HA; Beck DAC; Becraft ED; Beller HR; Beman JM; Bernier-Latmani R; Berry TD; Bertagnolli A; Bertilsson S; Bhatnagar JM; Bird JT; Blanchard JL; Blumer-Schuette SE; Bohannan B; Borton MA; Brady A; Brawley SH; Brodie J; Brown S; Brum JR; Brune A; Bryant DA; Buchan A; Buckley DH; Buongiorno J; Cadillo-Quiroz H; Caffrey SM; Campbell AN; Campbell B; Carr S; Carroll JL; Cary SC; Cates AM; Cattolico RA; Cavicchioli R; Chistoserdova L; Coleman ML; Constant P; Conway JM; Mac Cormack WP; Crowe S; Crump B; Currie C; Daly R; DeAngelis KM; Denef V; Denman SE; Desta A; Dionisi H; Dodsworth J; Dombrowski N; Donohue T; Dopson M; Driscoll T; Dunfield P; Dupont CL; Dynarski KA; Edgcomb V; Edwards EA; Elshahed MS; Figueroa I, 2021, 'A genomic catalog of Earth’s microbiomes', Nature Biotechnology, vol. 39, pp. 499 - 509, http://dx.doi.org/10.1038/s41587-020-0718-6
    Journal articles | 2021
    Nayfach S; Roux S; Seshadri R; Udwary D; Varghese N; Schulz F; Wu D; Paez-Espino D; Chen IM; Huntemann M; Palaniappan K; Ladau J; Mukherjee S; Reddy TBK; Nielsen T; Kirton E; Faria JP; Edirisinghe JN; Henry CS; Jungbluth SP; Chivian D; Dehal P; Wood-Charlson EM; Arkin AP; Tringe SG; Visel A; Abreu H; Acinas SG; Allen E; Allen MA; Alteio LV; Andersen G; Anesio AM; Attwood G; Avila-Magaña V; Badis Y; Bailey J; Baker B; Baldrian P; Barton HA; Beck DAC; Becraft ED; Beller HR; Beman JM; Bernier-Latmani R; Berry TD; Bertagnolli A; Bertilsson S; Bhatnagar JM; Bird JT; Blanchard JL; Blumer-Schuette SE; Bohannan B; Borton MA; Brady A; Brawley SH; Brodie J; Brown S; Brum JR; Brune A; Bryant DA; Buchan A; Buckley DH; Buongiorno J; Cadillo-Quiroz H; Caffrey SM; Campbell AN; Campbell B; Carr S; Carroll JL; Cary SC; Cates AM; Cattolico RA; Cavicchioli R; Chistoserdova L; Coleman ML; Constant P; Conway JM; Mac Cormack WP; Crowe S; Crump B; Currie C; Daly R; DeAngelis KM; Denef V; Denman SE; Desta A; Dionisi H; Dodsworth J; Dombrowski N; Donohue T; Dopson M; Driscoll T; Dunfield P; Dupont CL; Dynarski KA; Edgcomb V; Edwards EA; Elshahed MS; Figueroa I, 2021, 'Author Correction: A genomic catalog of Earth’s microbiomes (Nature Biotechnology, (2021), 39, 4, (499-509), 10.1038/s41587-020-0718-6)', Nature Biotechnology, vol. 39, pp. 521, http://dx.doi.org/10.1038/s41587-021-00898-4
    Journal articles | 2021
    Nayfach S; Roux S; Seshadri R; Udwary D; Varghese N; Schulz F; Wu D; Paez-Espino D; Chen IM; Huntemann M; Palaniappan K; Ladau J; Mukherjee S; Reddy TBK; Nielsen T; Kirton E; Faria JP; Edirisinghe JN; Henry CS; Jungbluth SP; Chivian D; Dehal P; Wood-Charlson EM; Arkin AP; Tringe SG; Visel A; Abreu H; Acinas SG; Allen E; Allen MA; Andersen G; Anesio AM; Attwood G; Avila-Magaña V; Badis Y; Bailey J; Baker B; Baldrian P; Barton HA; Beck DAC; Becraft ED; Beller HR; Beman JM; Bernier-Latmani R; Berry TD; Bertagnolli A; Bertilsson S; Bhatnagar JM; Bird JT; Blumer-Schuette SE; Bohannan B; Borton MA; Brady A; Brawley SH; Brodie J; Brown S; Brum JR; Brune A; Bryant DA; Buchan A; Buckley DH; Buongiorno J; Cadillo-Quiroz H; Caffrey SM; Campbell AN; Campbell B; Carr S; Carroll JL; Cary SC; Cates AM; Cattolico RA; Cavicchioli R; Chistoserdova L; Coleman ML; Constant P; Conway JM; Mac Cormack WP; Crowe S; Crump B; Currie C; Daly R; Denef V; Denman SE; Desta A; Dionisi H; Dodsworth J; Dombrowski N; Donohue T; Dopson M; Driscoll T; Dunfield P; Dupont CL; Dynarski KA; Edgcomb V; Edwards EA; Elshahed MS; Figueroa I; Flood B; Fortney N; Fortunato CS, 2021, 'Publisher Correction: A genomic catalog of Earth’s microbiomes (Nature Biotechnology, (2021), 39, 4, (499-509), 10.1038/s41587-020-0718-6)', Nature Biotechnology, vol. 39, pp. 520, http://dx.doi.org/10.1038/s41587-020-00769-4
    Journal articles | 2021
    Panwar P; Allen MA; Williams TJ; Haque S; Brazendale S; Hancock AM; Paez-Espino D; Cavicchioli R, 2021, 'Remarkably coherent population structure for a dominant Antarctic Chlorobium species', Microbiome, vol. 9, http://dx.doi.org/10.1186/s40168-021-01173-z
    Journal articles | 2021
    Roux S; Paul BG; Bagby SC; Nayfach S; Allen MA; Attwood G; Cavicchioli R; Chistoserdova L; Gruninger RJ; Hallam SJ; Hernandez ME; Hess M; Liu WT; McAllister TA; O’Malley MA; Peng X; Rich VI; Saleska SR; Eloe-Fadrosh EA, 2021, 'Ecology and molecular targets of hypermutation in the global microbiome', Nature Communications, vol. 12, pp. 3076, http://dx.doi.org/10.1038/s41467-021-23402-7
    Journal articles | 2021
    Shen L; Liu Y; Allen MA; Xu B; Wang N; Williams TJ; Wang F; Zhou Y; Liu Q; Cavicchioli R, 2021, 'Linking genomic and physiological characteristics of psychrophilic Arthrobacter to metagenomic data to explain global environmental distribution', Microbiome, vol. 9, pp. 136, http://dx.doi.org/10.1186/s40168-021-01084-z
    Journal articles | 2021
    Williams TJ; Allen MA; Berengut JF; Cavicchioli R, 2021, 'Shedding Light on Microbial “Dark Matter”: Insights Into Novel Cloacimonadota and Omnitrophota From an Antarctic Lake', Frontiers in Microbiology, vol. 12, pp. 741077, http://dx.doi.org/10.3389/fmicb.2021.741077
    Journal articles | 2021
    Williams TJ; Allen MA; Ivanova N; Huntemann M; Haque S; Hancock AM; Brazendale S; Cavicchioli R, 2021, 'Genome Analysis of a Verrucomicrobial Endosymbiont With a Tiny Genome Discovered in an Antarctic Lake', Frontiers in Microbiology, vol. 12, http://dx.doi.org/10.3389/fmicb.2021.674758
    Journal articles | 2020
    Panwar P; Allen MA; Williams TJ; Hancock AM; Brazendale S; Bevington J; Roux S; Páez-Espino D; Nayfach S; Berg M; Schulz F; Chen IMA; Huntemann M; Shapiro N; Kyrpides NC; Woyke T; Eloe-Fadrosh EA; Cavicchioli R, 2020, 'Influence of the polar light cycle on seasonal dynamics of an Antarctic lake microbial community', Microbiome, vol. 8, pp. 116, http://dx.doi.org/10.1186/s40168-020-00889-8
    Journal articles | 2020
    Roux S; Paul BG; Bagby SC; Allen MA; Attwood G; Cavicchioli R; Chistoserdova L; Hallam SJ; Hernandez ME; Hess M; Liu W-T; O’Malley MA; Peng X; Rich VI; Saleska S; Eloe-Fadrosh EA, 2020, 'Ecology and molecular targets of hypermutation in the global microbiome', , http://dx.doi.org/10.1101/2020.04.01.020958
    Journal articles | 2019
    Hamm JN; Erdmann S; Eloe-Fadrosh EA; Angeloni A; Zhong L; Brownlee C; Williams TJ; Barton K; Carswell S; Smith MA; Brazendale S; Hancock AM; Allen MA; Raftery MJ; Cavicchioli R, 2019, 'Unexpected host dependency of Antarctic Nanohaloarchaeota', Proceedings of the National Academy of Sciences of the United States of America, vol. 116, pp. 14661 - 14670, http://dx.doi.org/10.1073/pnas.1905179116
    Journal articles | 2019
    Williams TJ; Allen MA; Liao Y; Raftery MJ; Cavicchioli R, 2019, 'Sucrose metabolism in haloarchaea: Reassessment using genomics, proteomics, and metagenomics', Applied and Environmental Microbiology, vol. 85, http://dx.doi.org/10.1128/AEM.02935-18
    Journal articles | 2018
    Tschitschko B; Erdmann S; DeMaere MZ; Roux S; Panwar P; Allen MA; Williams TJ; Brazendale S; Hancock AM; Eloe-Fadrosh EA; Cavicchioli R, 2018, 'Genomic variation and biogeography of Antarctic haloarchaea', Microbiome, vol. 6, http://dx.doi.org/10.1186/s40168-018-0495-3
    Journal articles | 2017
    Allen MA; Cavicchioli R, 2017, 'Microbial communities of aquatic environments on Heard Island characterized by pyrotag sequencing and environmental data', Scientific Reports, vol. 7, http://dx.doi.org/10.1038/srep44480
    Journal articles | 2017
    Williams TJ; Allen M; Tschitschko B; Cavicchioli R, 2017, 'Glycerol metabolism of haloarchaea', Environmental Microbiology, vol. 19, pp. 864 - 877, http://dx.doi.org/10.1111/1462-2920.13580
    Journal articles | 2016
    Tschitschko B; Williams TJ; Allen MA; Zhong L; Raftery MJ; Cavicchioli R, 2016, 'Ecophysiological distinctions of haloarchaea from a hypersaline Antarctic lake determined using metaproteomics.', Appl Environ Microbiol, vol. 82, pp. 3165 - 3173, http://dx.doi.org/10.1128/AEM.00473-16
    Journal articles | 2015
    Tschitschko B; Williams TJ; Allen MA; Páez-Espino D; Kyrpides N; Zhong L; Raftery MJ; Cavicchioli R, 2015, 'Antarctic archaea–virus interactions: metaproteome-led analysis of invasion, evasion and adaptation', The ISME Journal, vol. 9, pp. 2094 - 2107, http://dx.doi.org/10.1038/ismej.2015.110
    Journal articles | 2014
    Williams TJ; Allen MA; DeMaere MZ; Kyrpides NC; Tringe SG; Woyke T; Cavicchioli R, 2014, 'Microbial ecology of an Antarctic hypersaline lake: genomic assessment of ecophysiology among dominant haloarchaea', ISME JOURNAL, vol. 8, pp. 1645 - 1658, http://dx.doi.org/10.1038/ismej.2014.65
    Journal articles | 2013
    Demaere MZ; Williams TJ; Allen MA; Brown MV; Gibson JAE; Rich J; Lauro FM; Dyall-Smith M; Davenport KW; Woyke T; Kyrpides NC; Tringe SG; Cavicchioli R, 2013, 'High level of intergenera gene exchange shapes the evolution of haloarchaea in an isolated Antarctic lake', Proceedings of the National Academy of Sciences of the United States of America, vol. 110, pp. 16939 - 16944, http://dx.doi.org/10.1073/pnas.1307090110
    Journal articles | 2013
    Siddiqui KS; Williams TJ; Wilkins D; Yau S; Allen MA; Brown MV; Lauro FM; Cavicchioli R, 2013, 'Psychrophiles', Annual Review of Earth and Planetary Sciences, vol. 41, pp. 87 - 115, http://dx.doi.org/10.1146/annurev-earth-040610-133514
    Journal articles | 2013
    Wilkins D; Yau S; Williams TJ; Allen MA; Brown MV; Demaere MZ; Lauro FM; Cavicchioli R, 2013, 'Key microbial drivers in Antarctic aquatic environments', FEMS Microbiology Reviews, vol. 37, pp. 303 - 335, http://dx.doi.org/10.1111/1574-6976.12007
    Journal articles | 2010
    Allen MA; Neilan BA; Burns BP; Jahnke LL; Summons RE, 2010, 'Lipid biomarkers in Hamelin Pool microbial mats and stromatolites', Organic Geochemistry, vol. 41, pp. 1207 - 1218, http://dx.doi.org/10.1016/j.orggeochem.2010.07.007
    Journal articles | 2009
    Allen MA; Goh F; Burns BP; Neilan BA, 2009, 'Bacterial, archaeal and eukaryotic diversity of smooth and pustular microbial mat communities in the hypersaline lagoon of Shark Bay', Geobiology, vol. 7, pp. 82 - 96, http://dx.doi.org/10.1111/j.1472-4669.2008.00187.x
    Journal articles | 2009
    Allen MA; Lauro FM; Williams TJ; Burg DW; Siddiqui KS; De Francisci D; Chong K; Pilak O; Chew H; De Maere M; Ting LL; Katrib M; Ng SC; Sowers KR; Galperin M; Anderson I; Ivanova N; Dalin E; Martinez MP; Lapidus A; Hauser L; Land MH; Thomas T; Cavicchioli R, 2009, 'The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: The role of genome evolution in cold adaptation', ISME Journal, vol. 3, pp. 1012 - 1035, http://dx.doi.org/10.1038/ismej.2009.45
    Journal articles | 2009
    Burns BP; Anitori R; Butterworth P; Henneberger R; Goh F; Allen MA; Ibanez-Peral R; Bergquist P; Walter MR; Neilan BA, 2009, 'Modern analogues and the early history of microbial life', Precambrian Research, vol. 173, pp. 10 - 18, http://dx.doi.org/10.1016/j.precamres.2009.05.006
    Journal articles | 2009
    Goh F; Allen MA; Leuko S; Kawaguchi T; Decho A; Burns BP; Neilan BA, 2009, 'Determining the specific microbial populations and their spatial distribution within the stromatolite ecosystem of Shark Bay', ISME Journal, vol. 3, pp. 383 - 396, http://dx.doi.org/10.1038/ismej.2008.114
    Journal articles | 2009
    Jungblut A; Allen MA; Burns BP; Neilan BA, 2009, 'Lipid biomarker analysis of cyanobacteria-dominated microbial mats in meltwater ponds on the McMurdo Ice Shelf, Antarctica', Organic Geochemistry, vol. 40, pp. 258 - 269, http://dx.doi.org/10.1016/j.orggeochem.2008.10.002
    Journal articles | 2008
    Allen MA; Goh QY; Leuko S; Igo A; Mizuki T; Usami R; Karnekura M; Neilan BA; Burns BP, 2008, 'Haloferax elongans sp nov and Haloterax mucosum sp nov., isolated from microbial mats from Hamelin Pool, Shark Bay, Australia', International Journal of Systematic and Evolutionary Microbiology, vol. 58, pp. 798 - 802, http://dx.doi.org/10.1099/ijs.0.65360-0
    Journal articles | 2007
    Leuko S; Goh F; Allen MA; Burns BP; Walter MR; Neilan BA, 2007, 'Analysis of intergenic spacer region length polymorphisms to investigate the halophilic archaeal diversity of stromatolites and microbial mats', Extremophiles, vol. 11, pp. 203 - 210, http://dx.doi.org/10.1007/s00792-006-0028-z
    Journal articles | 2006
    Goh QY; Leuko S; Allen MA; Bowman J; Kamekura M; Neilan BA; Burns BP, 2006, 'Halococcus hamelinensis sp nov., a novel halophilic archaeon isolated from stromatolites in Shark Bay, Australia', International Journal of Systematic and Evolutionary Microbiology, vol. 56, pp. 1323 - 1329, http://dx.doi.org/10.1099/ijs.0.64180-0
    Journal articles | 2004
    Burns BP; Goh QY; Allen MA; Neilan BA, 2004, 'Microbial diversity of extant stromatolites in the hypersaline marine environment of Shark Bay, Australia', Environmental Microbiology, vol. 6, pp. 1096 - 1101, http://dx.doi.org/10.1111/j.1462-2920.2004.00651.x
  • Preprints | 2020
    Shen L; Liu Y; Allen MA; Xu B; Wang N; Williams TJ; Wang F; Zhou Y; Liu Q; Cavicchioli R, 2020, Linking Genomic and Physiological Characteristics of Psychrophilic Arthrobacter to Metagenomic Data to Explain Global Environmental Distribution, http://dx.doi.org/10.21203/rs.3.rs-119482/v1
    Theses / Dissertations | 2007
    Allen MA, 2007, An astrobiology-focused analysis of microbial mat communities from Hamelin Pool, Shark Bay, Western Australia.