By Dr Michelle Allen

Journal articles

Kelliher JM; Mirzayi C; Bordenstein SR; Oliver A; Kellogg CA; Hatcher EL; Berg M; Baldrian P; Aljumaah M; Miller CML; Mungall C; Novak V; Palucki A; Smith E; Tabassum N; Bonito G; Brister JR; Chain PSG; Chen M; Degregori S; Dundore-Arias JP; Emerson JB; Moreira C. Fernandes V; Flores R; Gonzalez A; Hansen ZA; Jackson SA; Moustafa AM; Northen TR; Pariente N; Pett-Ridge J; Record S; Reji L; Reysenbach AL; Rich VI; Richardson L; Roux S; Schriml LM; Shabman RS; Sierra MA; Sullivan MB; Sundaramurthy P; Thibault KM; Thompson LR; Tighe S; Vereen E; Burcham ZM; Yeoh YK; Zhang Y; You Y; Peng X; Liu XJA; Anthony WE; Nelson W; Boulton W; Hervey WJ; Myers T; Mock T; Nelson TM; Woyke T; Chen S; Hodgkins S; Brawley SH; Mundra S; Yarwood SA; Tsola SL; Couvillion S; Jensen S; Moxon S; Roesemann S; Sanchez-Carrillo S; Baranzini SE; Oh S; Jungbluth SP; Finks SS; Garcia SL; Jackrel SL; Miller SN; ʻAnolani Alegado R; Wilhelm RC; Gruninger RJ; Knight R; White RA; Mondav R; Corrêa dos Santos RA; Longley R; Saho R; Reiss RA; Handakumbura PP; Sengupta P; Junier P; Pope PB; Pjevac P; Turnbaugh PJ; Cotter PD; Eyice O; Youssef NH; Segata N; Kriefall NG; Brereton NJB, 2025, 'STREAMS guidelines: standards for technical reporting in environmental and host-associated microbiome studies', Nature Microbiology, 10, pp. 3059 - 3068, http://dx.doi.org/10.1038/s41564-025-02186-2

Williams TJ; Allen MA; Ray AE; Benaud N; Chelliah DS; Albanese D; Donati C; Selbmann L; Coleine C; Ferrari BC, 2024, 'Novel endolithic bacteria of phylum Chloroflexota reveal a myriad of potential survival strategies in the Antarctic desert', Applied and Environmental Microbiology, 90, http://dx.doi.org/10.1128/aem.02264-23

Garritano AN; Zhang Z; Jia Y; Allen MA; Hill LJ; Kuzhiumparambil U; Hinkley C; Raina JB; Peixoto RS; Thomas T, 2024, 'Simple Porifera holobiont reveals complex interactions between the host, an archaeon, a bacterium, and a phage', Isme Journal, 18, http://dx.doi.org/10.1093/ismejo/wrae197

Panwar P; Williams TJ; Allen MA; Cavicchioli R, 2022, 'Population structure of an Antarctic aquatic cyanobacterium', Microbiome, 10, http://dx.doi.org/10.1186/s40168-022-01404-x

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, 24, pp. 2576 - 2603, http://dx.doi.org/10.1111/1462-2920.16026

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, 12, pp. 3076, http://dx.doi.org/10.1038/s41467-021-23402-7

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, 9, pp. 136, http://dx.doi.org/10.1186/s40168-021-01084-z

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, 9, http://dx.doi.org/10.1186/s40168-021-01173-z

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, 12, http://dx.doi.org/10.3389/fmicb.2021.741077

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, 12, pp. 674758, http://dx.doi.org/10.3389/fmicb.2021.674758

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; Williams T; Thomas T, 2021, 'A genomic catalog of Earth’s microbiomes', Nature Biotechnology, 39, pp. 499 - 509, http://dx.doi.org/10.1038/s41587-020-0718-6

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; Thomas T; Williams T, 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, 39, pp. 521, http://dx.doi.org/10.1038/s41587-021-00898-4

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; Williams T; Thomas T, 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, 39, pp. 520, http://dx.doi.org/10.1038/s41587-020-00769-4

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, 8, pp. 116, http://dx.doi.org/10.1186/s40168-020-00889-8

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, 85, pp. e02935 - e02918, http://dx.doi.org/10.1128/AEM.02935-18

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, 116, pp. 14661 - 14670, http://dx.doi.org/10.1073/pnas.1905179116

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, 6, pp. 113, http://dx.doi.org/10.1186/s40168-018-0495-3

Allen MA; Cavicchioli R, 2017, 'Microbial communities of aquatic environments on Heard Island characterized by pyrotag sequencing and environmental data', Scientific Reports, 7, pp. 44480, http://dx.doi.org/10.1038/srep44480

Williams TJ; Allen M; Tschitschko B; Cavicchioli R, 2017, 'Glycerol metabolism of haloarchaea', Environmental Microbiology, 19, pp. 864 - 877, http://dx.doi.org/10.1111/1462-2920.13580

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, 82, pp. 3165 - 3173, http://dx.doi.org/10.1128/AEM.00473-16

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, 9, pp. 2094 - 2107, http://dx.doi.org/10.1038/ismej.2015.110

Williams TJ; Allen MA; DeMaere MZ; Kyrpides NC; Tringe SG; Woyke T; Cavicchioli R, 2014, 'Erratum: Microbial ecology of an Antarctic hypersaline lake: genomic assessment of ecophysiology among dominant haloarchaea', The ISME Journal, 8, pp. 1752 - 1752, http://dx.doi.org/10.1038/ismej.2014.65

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, 8, pp. 1645 - 1658, http://dx.doi.org/10.1038/ismej.2014.65

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.', Proc Natl Acad Sci U S A, 110, pp. 16939 - 16944, http://dx.doi.org/10.1073/pnas.1307090110

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, 37, pp. 303 - 335, http://dx.doi.org/10.1111/1574-6976.12007

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, 41, pp. 87 - 115, http://dx.doi.org/10.1146/annurev-earth-040610-133514

Allen MA; Neilan BA; Burns BP; Jahnke LL; Summons RE, 2010, 'Lipid biomarkers in Hamelin Pool microbial mats and stromatolites', Organic Geochemistry, 41, pp. 1207 - 1218, http://dx.doi.org/10.1016/j.orggeochem.2010.07.007

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, 7, pp. 82 - 96

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, 3, pp. 383 - 396

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, 40, pp. 258 - 269

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, 173, pp. 10 - 18

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, 3, pp. 1012 - 1035

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, 58, pp. 798 - 802, http://dx.doi.org/10.1099/ijs.0.65360-0

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, 11, pp. 203 - 210

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, 56, pp. 1323 - 1329

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, 6, pp. 1096 - 1101

ALLEN MA; WRENN JM; BORZELLECA JF, 1978, 'STUDY OF MECHANISM OF TRANSPORT OF BENZYLPENICILLIN IN RAT SUB-MAXILLARY GLAND', ARCHIVES INTERNATIONALES DE PHARMACODYNAMIE ET DE THERAPIE, 233, pp. 180 - 191

Conference Papers

Herndon J; Hayden D; Campion J; Cousineau V; Allen M; Rodgers P; ElGabry E, 2020, 'Computer Learning Platform Utility for Standardized Biomarker Training', in LABORATORY INVESTIGATION, NATURE PUBLISHING GROUP, CA, Los Angeles, pp. 538 - 538, presented at 109th Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology (USCAP), CA, Los Angeles, 29 February 2020 - 05 March 2020

Herndon J; Hayden D; Campion J; Cousineau V; Allen M; Rodgers P; ElGabry E, 2020, 'Computer Learning Platform Utility for Standardized Biomarker Training', in MODERN PATHOLOGY, SPRINGERNATURE, CA, Los Angeles, pp. 538 - 538, presented at 109th Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology (USCAP), CA, Los Angeles, 29 February 2020 - 05 March 2020

Hayden D; Herndon J; Campion J; Bai I; Newell AH; Allen M; ElGabry E; Rodgers P, 2020, 'Glass to Digital Concordance: The Computer Learning Platform Experience with Multiple Biomarkers', in LABORATORY INVESTIGATION, NATURE PUBLISHING GROUP, CA, Los Angeles, pp. 535 - 536, presented at 109th Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology (USCAP), CA, Los Angeles, 29 February 2020 - 05 March 2020

Hayden D; Herndon J; Campion J; Bai I; Newell AH; Allen M; ElGabry E; Rodgers P, 2020, 'Glass to Digital Concordance: The Computer Learning Platform Experience with Multiple Biomarkers', in MODERN PATHOLOGY, SPRINGERNATURE, CA, Los Angeles, pp. 535 - 536, presented at 109th Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology (USCAP), CA, Los Angeles, 29 February 2020 - 05 March 2020

ALLEN MA; BORZELLECA JF, 1974, 'DIPHENYLHYDANTOIN DISTRIBUTION IN RAT SUBMAXILLARY-GLAND - INFLUENCE OF AGE', in FEDERATION PROCEEDINGS, FEDERATION AMER SOC EXP BIOL, pp. 525 - 525

ALLEN MA; BORZELLE JF, 1973, 'METHOD OF BENZYLPENICILLIN-C-14 POTASSIUM DISTRIBUTION IN RAT SUBMAXILLARY-GLAND', in FEDERATION PROCEEDINGS, FEDERATION AMER SOC EXP BIOL, pp. 733 - &

MILLER DW; SLATER JM; AWSCHALOM MW; ALLEN MA, 'DESIGN OF A HOSPITAL-BASED PROTON-BEAM THERAPY CENTER', in MEDICAL PHYSICS, AMER INST PHYSICS, pp. 468 - 468

Theses / Dissertations

Allen MA, 2007, An astrobiology-focused analysis of microbial mat communities from Hamelin Pool, Shark Bay, Western Australia.

Working Papers

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, Cold Spring Harbor Laboratory, http://dx.doi.org10.1101/2020.04.01.020958

Media

, Remarkably coherent population structure for a dominant Antarctic Chlorobium species, Springer Science and Business Media LLC, http://dx.doi.org/10.21203/rs.3.rs-1405943/v1

Preprints

Shen L; Liu Y; Allen MA; Xu B; Wang N; Williams TJ; Wang F; Zhou Y; Liu Q; Cavicchioli R, 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

Hewage SA; Senanayake SJ; Brain D; Allen M; McPhail S; Parsonage W; Walters T; Kularatna S, Preferences for mobile app features to support people living with chronic heart diseases: A discrete choice study. (Preprint), http://dx.doi.org/10.2196/preprints.58556

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