Select Publications

Books

2007, Archaea: Molecular and Cellular Biology, Cavicchioli R, (ed.), ASM Press, USA

Book Chapters

Woese CR, 2007, 'The Archaea: an Invitation to Evolution', in Cavicchioli R (ed.), ARCHAEA: MOLECULAR AND CELLULAR BIOLOGY, AMER SOC MICROBIOLOGY, pp. 1 - 13, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000278887900002&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Cavicchioli R; Curmi PMG; Siddiqui KS; Thomas T, 2006, '17 Proteins from Psychrophiles', in Methods in Microbiology, Elsevier, pp. 395 - 436, http://dx.doi.org/10.1016/s0580-9517(08)70020-5

Cavicchioli R; Goodchild A; Raftery M, 2005, 'Proteomics of Archaea', in Microbial Proteomics: Functional Biology of Whole Organisms, pp. 57 - 72, http://dx.doi.org/10.1002/0471973165.ch5

Journal articles

Pavlopoulos GA; Baltoumas FA; Liu S; Selvitopi O; Camargo AP; Nayfach S; Azad A; Roux S; Call L; Ivanova NN; Chen IM; Paez-Espino D; Karatzas E; Acinas SG; Ahlgren N; Attwood G; Baldrian P; Berry T; Bhatnagar JM; Bhaya D; Bidle KD; Blanchard JL; Boyd ES; Bowen JL; Bowman J; Brawley SH; Brodie EL; Brune A; Bryant DA; Buchan A; Cadillo-Quiroz H; Campbell BJ; Cavicchioli R; Chuckran PF; Coleman M; Crowe S; Colman DR; Currie CR; Dangl J; Delherbe N; Denef VJ; Dijkstra P; Distel DD; Eloe-Fadrosh E; Fisher K; Francis C; Garoutte A; Gaudin A; Gerwick L; Godoy-Vitorino F; Guerra P; Guo J; Habteselassie MY; Hallam SJ; Hatzenpichler R; Hentschel U; Hess M; Hirsch AM; Hug LA; Hultman J; Hunt DE; Huntemann M; Inskeep WP; James TY; Jansson J; Johnston ER; Kalyuzhnaya M; Kelly CN; Kelly RM; Klassen JL; Nüsslein K; Kostka JE; Lindow S; Lilleskov E; Lynes M; Mackelprang R; Martin FM; Mason OU; McKay RM; McMahon K; Mead DA; Medina M; Meredith LK; Mock T; Mohn WW; Moran MA; Murray A; Neufeld JD; Neumann R; Norton JM; Partida-Martinez LP; Pietrasiak N; Pelletier D; Reddy TBK; Reese BK; Reichart NJ; Reiss R; Saito MA; Schachtman DP; Seshadri R, 2023, 'Unraveling the functional dark matter through global metagenomics', Nature, 622, pp. 594 - 602, http://dx.doi.org/10.1038/s41586-023-06583-7

Lappan R; Shelley G; Islam ZF; Leung PM; Lockwood S; Nauer PA; Jirapanjawat T; Ni G; Chen YJ; Kessler AJ; Williams TJ; Cavicchioli R; Baltar F; Cook PLM; Morales SE; Greening C, 2023, 'Molecular hydrogen in seawater supports growth of diverse marine bacteria', Nature Microbiology, 8, pp. 581 - 595, http://dx.doi.org/10.1038/s41564-023-01322-0

Le Lay C; Hamm JN; Williams TJ; Shi M; Cavicchioli R; Holmes EC, 2023, 'Viral community composition of hypersaline lakes', Virus Evolution, 9, http://dx.doi.org/10.1093/ve/vead057

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

Fremin BJ; Bhatt AS; Kyrpides NC; Sengupta A; Sczyrba A; Maria da Silva A; Buchan A; Gaudin A; Brune A; Hirsch AM; Neumann A; Shade A; Visel A; Campbell B; Baker B; Hedlund BP; Crump BC; Currie C; Kelly C; Craft C; Hazard C; Francis C; Schadt CW; Averill C; Mobilian C; Buckley D; Hunt D; Noguera D; Beck D; Valentine DL; Walsh D; Sumner D; Lymperopoulou D; Bhaya D; Bryant DA; Morrison E; Brodie E; Young E; Lilleskov E; Högfors-Rönnholm E; Chen F; Stewart F; Nicol GW; Teeling H; Beller HR; Dionisi H; Liao HL; Beman JM; Stegen J; Tiedje J; Jansson J; VanderGheynst J; Norton J; Dangl J; Blanchard J; Bowen J; Macalady J; Pett-Ridge J; Rich J; Payet JP; Gladden JD; Raff JD; Klassen JL; Tarn J; Neufeld J; Gravuer K; Hofmockel K; Chen KH; Konstantinidis K; DeAngelis KM; Partida-Martinez LP; Meredith L; Chistoserdova L; Moran MA; Scarborough M; Schrenk M; Sullivan M; David M; O'Malley MA; Medina M; Habteselassie M; Ward ND; Pietrasiak N; Mason OU; Sorensen PO; Estrada de los Santos P; Baldrian P; McKay RM; Simister R; Stepanauskas R; Neumann R; Malmstrom R; Cavicchioli R; Kelly R; Hatzenpichler R; Stocker R; Cattolico RA; Ziels R; Vilgalys R; Blumer-Schuette S, 2022, 'Thousands of small, novel genes predicted in global phage genomes', Cell Reports, 39, http://dx.doi.org/10.1016/j.celrep.2022.110984

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, 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, 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, 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, 2021, 'A genomic catalog of Earth’s microbiomes', Nature Biotechnology, 39, pp. 499 - 509, http://dx.doi.org/10.1038/s41587-020-0718-6

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

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

Cavicchioli R; Ripple WJ; Timmis KN; Azam F; Bakken LR; Baylis M; Behrenfeld MJ; Boetius A; Boyd PW; Classen AT; Crowther TW; Danovaro R; Foreman CM; Huisman J; Hutchins DA; Jansson JK; Karl DM; Koskella B; Mark Welch DB; Martiny JBH; Moran MA; Orphan VJ; Reay DS; Remais JV; Rich VI; Singh BK; Stein LY; Stewart FJ; Sullivan MB; van Oppen MJH; Weaver SC; Webb EA; Webster NS, 2019, 'Scientists’ warning to humanity: microorganisms and climate change', Nature Reviews Microbiology, 17, pp. 569 - 586, http://dx.doi.org/10.1038/s41579-019-0222-5

Timmis K; Cavicchioli R; Garcia JL; Nogales B; Chavarría M; Stein L; McGenity TJ; Webster N; Singh BK; Handelsman J; de Lorenzo V; Pruzzo C; Timmis J; Martín JLR; Verstraete W; Jetten M; Danchin A; Huang W; Gilbert J; Lal R; Santos H; Lee SY; Sessitsch A; Bonfante P; Gram L; Lin RTP; Ron E; Karahan ZC; van der Meer JR; Artunkal S; Jahn D; Harper L, 2019, 'The urgent need for microbiology literacy in society', Environmental Microbiology, 21, pp. 1513 - 1528, http://dx.doi.org/10.1111/1462-2920.14611

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, http://dx.doi.org/10.1128/AEM.02935-18

Cavicchioli R, 2019, 'A vision for a ‘microbcentric’ future', Microbial Biotechnology, 12, pp. 26 - 29, http://dx.doi.org/10.1111/1751-7915.13262

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

2018, 'Extreme Excitement about Archaea', Cell, 172, pp. 1153 - 1154, http://dx.doi.org/10.1016/j.cell.2018.02.038

Erdmann S; Tschitschko B; Zhong L; Raftery MJ; Cavicchioli R, 2017, 'A plasmid from an Antarctic haloarchaeon uses specialized membrane vesicles to disseminate and infect plasmid-free cells', Nature Microbiology, 2, pp. 1446 - 1455, http://dx.doi.org/10.1038/s41564-017-0009-2

Williams TJ; Liao Y; Ye J; Kuchel RP; Poljak A; Raftery MJ; Cavicchioli R, 2017, 'Cold adaptation of the Antarctic haloarchaea Halohasta litchfieldiae and Halorubrum lacusprofundi', Environmental Microbiology, 19, pp. 2210 - 2227, http://dx.doi.org/10.1111/1462-2920.13705

Jayawardena MB; Yee LH; Poljak A; Cavicchioli R; Kjelleberg SJ; Siddiqui KS, 2017, 'Enhancement of lipase stability and productivity through chemical modification and its application to latex-based polymer emulsions', Process Biochemistry, 57, pp. 131 - 140, http://dx.doi.org/10.1016/j.procbio.2017.03.014

Allen MA; Cavicchioli R, 2017, 'Microbial communities of aquatic environments on Heard Island characterized by pyrotag sequencing and environmental data', Scientific Reports, 7, 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

Paez-Espino D; Chen IMA; Palaniappan K; Ratner A; Chu K; Szeto E; Pillay M; Huang J; Markowitz VM; Nielsen T; Huntemann M; Reddy TBK; Pavlopoulos GA; Sullivan MB; Campbell BJ; Chen F; McMahon K; Hallam SJ; Denef V; Cavicchioli R; Caffrey SM; Streit WR; Webster J; Handley KM; Salekdeh GH; Tsesmetzis N; Setubal JC; Pope PB; Liu WT; Rivers AR; Ivanova NN; Kyrpides NC, 2017, 'IMG/VR: A database of cultured and uncultured DNA viruses and retroviruses', Nucleic Acids Research, 45, pp. D457 - D465, http://dx.doi.org/10.1093/nar/gkw1030

Liao Y; Williams TJ; Ye J; Charlesworth J; Burns BP; Poljak A; Raftery MJ; Cavicchioli R, 2016, 'Morphological and proteomic analysis of biofilms from the Antarctic archaeon, Halorubrum lacusprofundi', Scientific Reports, 6, http://dx.doi.org/10.1038/srep37454

Liao Y; Williams TJ; Walsh JC; Ji M; Poljak A; Curmi PMG; Duggin IG; Cavicchioli R, 2016, 'Developing a genetic manipulation system for the Antarctic archaeon, Halorubrum lacusprofundi: Investigating acetamidase gene function', Scientific Reports, 6, http://dx.doi.org/10.1038/srep34639

Danovaro R; Dell'anno A; Corinaldesi C; Rastelli E; Cavicchioli R; Krupovic M; Noble RT; Nunoura T; Prangishvili D, 2016, 'Virus-mediated archaeal hecatomb in the deep seafloor', Science Advances, 2, http://dx.doi.org/10.1126/sciadv.1600492

Anderson IJ; DasSarma P; Lucas S; Copeland A; Lapidus A; Del Rio TG; Tice H; Dalin E; Bruce DC; Goodwin L; Pitluck S; Sims D; Brettin TS; Detter JC; Han CS; Larimer F; Hauser L; Land M; Ivanova N; Richardson P; Cavicchioli R; DasSarma S; Woese CR; Kyrpides NC, 2016, 'Complete genome sequence of the Antarctic Halorubrum lacusprofundi type strain ACAM 34', Standards in Genomic Sciences, 11, http://dx.doi.org/10.1186/s40793-016-0194-2

Taha ; Siddiqui KS; Campanaro S; Najnin T; Deshpande N; Williams TJ; Aldrich-Wright J; Wilkins M; Curmi PMG; Cavicchioli R, 2016, 'Single TRAM domain RNA-binding proteins in Archaea: functional insight from Ctr3 from the Antarctic methanogen Methanococcoides burtonii', Environmental microbiology, 18, pp. 2810 - 2824, http://dx.doi.org/10.1111/1462-2920.13229

Najnin T; Siddiqui KS; Taha ; Elkaid N; Kornfeld G; Curmi PMG; Cavicchioli R, 2016, 'Characterization of a temperature-responsive two component regulatory system from the Antarctic archaeon, Methanococcoides burtonii', Scientific Reports, 6, http://dx.doi.org/10.1038/srep24278

Richards SL; Cawley AT; Cavicchioli R; Suann CJ; Pickford R; Raftery MJ, 2016, 'Aptamer based peptide enrichment for quantitative analysis of gonadotropin-releasing hormone by LC-MS/MS', Talanta, 150, pp. 671 - 680, http://dx.doi.org/10.1016/j.talanta.2016.01.006

Cavicchioli R, 2016, 'On the concept of a psychrophile', ISME Journal, 10, pp. 793 - 795, http://dx.doi.org/10.1038/ismej.2015.160

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

Cavicchioli R, 2015, 'Microbial ecology of Antarctic aquatic systems', Nature Reviews Microbiology, 13, pp. 691 - 706, http://dx.doi.org/10.1038/nrmicro3549

Cavicchioli R; Erdmann S, 2015, 'The discovery of Antarctic RNA viruses: A new game changer', Molecular Ecology, 24, pp. 4809 - 4811, http://dx.doi.org/10.1111/mec.13387

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

Sun T; Socki RA; Bish DL; Harvey RP; Bao H; Niles PB; Cavicchioli R; Tonui E, 2015, 'Lost cold Antarctic deserts inferred from unusual sulfate formation and isotope signatures', Nature Communications, 6, http://dx.doi.org/10.1038/ncomms8579

Ertan H; Cassel C; Verma A; Poljak A; Charlton T; Aldrich-Wright J; Omar SM; Siddiqui KS; Cavicchioli R, 2015, 'A new broad specificity alkaline metalloprotease from a Pseudomonas sp. isolated from refrigerated milk: Role of calcium in improving enzyme productivity', Journal of Molecular Catalysis B: Enzymatic, 113, pp. 1 - 8, http://dx.doi.org/10.1016/j.molcatb.2014.12.010

Luk AWS; Williams TJ; Erdmann S; Thane Papke R; Cavicchioli R, 2014, 'Viruses of haloarchaea', Life, 4, pp. 681 - 715, http://dx.doi.org/10.3390/life4040681

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

Williams TJ; Cavicchioli R, 2014, 'Marine metaproteomics: Deciphering the microbial metabolic food web', Trends in Microbiology, 22, pp. 248 - 260, http://dx.doi.org/10.1016/j.tim.2014.03.004

Siddiqui KS; Ertan H; Charlton T; Poljakc A; Khaled AK; Yang X; Marshall G; Cavicchioli R, 2014, 'Versatile peroxidase degradation of humic substances: Use of isothermal titration calorimetry to assess kinetics, and applications to industrial wastes', Journal of Biotechnology, 178, pp. 1 - 11

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, 110, pp. 16939 - 16944, http://dx.doi.org/10.1073/pnas.1307090110


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