Publications

117 entries « 2 of 3 »

2017

RM, Bowers; NC, Kyrpides; R, Stepanauskas; M, Harmon-Smith; D, Doud; TBK, Reddy; F, Schulz; J, Jarett; AR, Rivers; EA, Eloe-Fadrosh; SG, Tringe; NN, Ivanova; A, Copeland; A, Clum; ED, Becraft; RR, Malmstrom; B, Birren; M, Podar; P, Bork; GM, Weinstock; GM, Garrity; JA, Dodsworth; S, Yooseph; G, Sutton; FO, Glöckner; JA, Gilbert; WC, Nelson; SJ, Hallam; SP, Jungbluth; TJG, Ettema; S, Tighe; KT, Konstantinidis; WT, Liu; BJ, Baker; T, Rattei; JA, Eisen; B, Hedlund; KD, McMahon; N, Fierer; R, Knight; R, Finn; G, Cochrane; I, Karsch-Mizrachi; GW, Tyson; C, Rinke; A, Lapidus; F, Meyer; P, Yilmaz; DH, Parks; AM, Eren; L, Schriml; JF, Banfield; P, Hugenholtz; T, Woyke

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea Journal Article

In: Nature Biotechnology, vol. 35, pp. 725-731, 2017.

Abstract | Links | BibTeX

A, Alberti; J, Poulain; S, Engelen; K, Labadie; S, Romac; I, Ferrera; G, Albini; JM, Aury; C, Belser; A, Bertrand; C, Cruaud; C, Da Silva; C, Dossat; F, Gavory; S, Gas; J, Guy; M, Haquelle; E, Jacoby; O, Jaillon; A, Lemainque; E, Pelletier; G, Samson; M, Wessner; SG, Acinas; M, Royo-Llonch; FM, Cornejo-Castillo; R, Logares; B, Fernández-Gómez; C, Bowler; G, Cochrane; C, Amid; PT, Hoopen; C, De Vargas; N, Grimsley; E, Desgranges; S, Kandels-Lewis; H, Ogata; N, Poulton; ME, Sieracki; R, Stepanauskas; MB, Sullivan; JR, Brum; MB, Duhaime; BT, Poulos; BL, Hurwitz; S, Pesant; E, Karsenti; P, Wincker; P, Bazire; O, Beluche; L, Bertrand; M, Besnard-Gonnet; I, Bordelais; M, Boutard; M, Dubois; C, Dumont; E, Ettedgui; P, Fernandez; E, Garcia; NG, Aiach; T, Guerin; C, Hamon; E, Brun; S, Lebled; P, Lenoble; C, Louesse; E, Mahieu; B, Mairey; N, Martins; C, Megret; C, Milani; J, Muanga; C, Orvain; E, Payen; P, Perroud; E, Petit; D, Robert; M, Ronsin; B, Vacherie; P, Bork; E, Boss; M, Follows; G, Gorsky; P, Hingamp; D, Iudicone; L, Karp-Boss; F, Not; J, Raes; C, Sardet; S, Speich; L, Stemmann; S, Sunagawa

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition Journal Article

In: Scientific Data, vol. 4, 2017.

Abstract | Links | BibTeX

M, Royo-Llonch; I, Ferrera; FM, Cornejo-Castillo; P, Sánchez; G, Salazar; R, Stepanauskas; JM, González; ME, Sieracki; S, Speich; L, Stemmann; C, Pedrós-Alió; SG, Acinas

Exploring microdiversity in novel Kordia sp. (Bacteroidetes) with proteorhodopsin from the tropical Indian Ocean via Single Amplified Genomes Journal Article

In: Frontiers in Microbiology, vol. 8, 2017.

Abstract | Links | BibTeX

R, Stepanauskas; EA, Fergusson; J, Brown; NJ, Poulton; B, Tupper; JM, Labonté; ED, Becraft; JM, Brown; MJ, Pachiadaki; T, Povilaitis; BP, Thompson; CJ, Mascena; WK, Bellows; A, Lubys

Improved genome recovery and integrated cell-size analyses of individual uncultured microbial cells and viral particles Journal Article

In: Nature Communications, vol. 8, no. 84, 2017.

Abstract | Links | BibTeX

A, Collingro; S, Köstlbacher; M, Mussmann; R, Stepanauskas; S, Hallam; M, Horn

Unexpected genomic features in widespread intracellular bacteria: evidence for motility of marine chlamydiae Journal Article

In: ISME, 2017.

Abstract | Links | BibTeX

Luo, Haiwei; Huang, Yongjie; Stepanauskas, Ramunas; Tang, Jijun

Excess of non-conservative amino acid changes in marine bacterioplankton lineages with reduced genomes Journal Article

In: Nature Microbiology, vol. 2, no. 17091, 2017.

Abstract | Links | BibTeX

N, Kashtan; SE, Roggensack; JW, Berta-Thompson; M, Grinberg; R, Stepanauskas; SW, Chisholm

Fundamental differences in diversity and genomic population structure between Atlantic and Pacific Prochlorococcus Journal Article

In: ISME, 2017.

Abstract | Links | BibTeX

WH, Wilson; IC, Gilg; M, Moniruzzaman; EK, Field; S, Koren; GR, LeCleir; J, Martínez Martínez; NJ, Poulton; BK, Swan; R, Stepanauskas; SW, Wilhelm

Genomic exploration of individual giant ocean viruses Journal Article

In: ISME, 2017.

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Y, Guan; MF, Haroon; I, Alam; JG, Ferry; U, Stingl

Single-cell genomics reveals pyrrolysine-encoding potential in members of uncultivated archaeal candidate division MSBL1 Journal Article

In: vol. 9, no. 4, pp. 404-410, 2017.

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Z, Landry; BK, Swan; GJ, Herndl; R, Stepanauskas; SJ, Giovannoni

SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter Journal Article

In: mBio, 2017.

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SP, Jungbluth; del Rio TG,; SG, Tringe; R, Stepanauskas; MS, Rappé

Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems Journal Article

In: PeerJ, 2017.

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P, Starnawski; T, Bataillon; T.J.G, Ettema; L.M, Jochum; Schreiber L,; X, Chen; Ploz M Lever M, Jørgensen B; A, Schramm; K, Kjeldsen

Microbial community assembly and evolution in subseafloor sediment Journal Article

In: PNAS, vol. 114, no. 11, pp. 2940-2945, 2017.

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JF, Mangot; R, Logares; P, Sanchez; F, Latorre; Y, Seeleuthner; S, Mondy; ME, Sieracki; O, Jaillon; P, Wincker; C, Vargas; R, Massana

Accessing the genomic information of unculturable oceanic picoeukaryotes by combining multiple single cells Journal Article

In: Scientific Reports, vol. 7, no. 41498, 2017.

Abstract | Links | BibTeX

MJ, Neave; CT, Michell; A, Apprill; CR, Voolstra

Endozoicomonas genomes reveal functional adaptation and plasticity in bacterial strains symbiotically associated with diverse marine hosts Journal Article

In: Scientific Reports, vol. 7, no. 40579, 2017.

Abstract | Links | BibTeX

2016

J, Choi; F, Yang; R, Stepanauskas; E, Cardenas; A, Garoutte; R, Williams; J, Flater; JM, Tiedje; KS, Hofmockel; 6,; B, Gelder; A, Howe

Strategies to improve reference databases for soil microbiomes Journal Article

In: ISME, 2016.

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T, Vannier; J, Leconte; Y, Seeleuthner; S, Mondy; E, Pelletier; JM, Aury; C, De Vargas; M, Sieracki; D, Iudicone; D, Vaulot; P, Wincker; O, Jaillon

Survey of the green picoalga Bathycoccus genomes in the global ocean Journal Article

In: Scientific Reports, vol. 6, 2016.

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MJ, Neave; R, Rachmawati; L, Xun; CT, Michell; DG, Bourne; A, Apprill; CR, Voolstra

Differential specificity between closely related corals and abundant Endozoicomonas endosymbionts across global scales Journal Article

In: ISME, 2016.

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MJ, Neave; R, Rachmawati; L, Xun; CT, Michell; DG, Bourne; A, Apprill; CR, Voolstra

Differential specificity between closely related corals and abundant Endozoicomonas endosymbionts across global scales Journal Article

In: The ISME Journal, vol. 11, pp. 186-200, 2016.

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K, Wasmund; M, Cooper; L, Schreiber; KG, Lloyd; BJ, Baker; DJ, Petersen; BB, Jørgensen; R, Stepanauskas; R, Reinhardt; A, Schramm; A, Loy; L, Adrian

Single-Cell Genome and Group-Specific dsrAB Sequencing Implicate Marine Members of the Class Dehalococcoidia (Phylum Chloroflexi) in Sulfur Cycling Journal Article

In: mBio, vol. 7, no. 3, 2016.

Abstract | Links | BibTeX

H, Fullerton; CL, Moyer

Comparative Single-Cell Genomics of Chloroflexi from the Okinawa Trough Deep Subsurface Biosphere Journal Article

In: Applied and Environmental Microbiology, vol. 82, pp. 3000-3008, 2016.

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BJ, Baker; JH, Saw; AE, Lind; CS, Lazar; KU, Hinrichs; AP, Teske; TJ, Ettema

Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea Journal Article

In: Nature Microbiology, vol. 1, no. 16002, 2016.

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S, Dyksma; K, Bischof; BM, Fuchs; K, Hoffmann; D, Meier; A, Meyerdierks; P, Pjevac; D, Probandt; M, Richter; R, Stepanauskas; M, Mußmann

Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments Journal Article

In: ISME, vol. 10, pp. 1939–1953, 2016.

Abstract | Links | BibTeX

Y, Zhang; Y, Sun; N, Jiao; R, Stepanauskas; H, Luo

Ecological Genomics of the Uncultivated Marine Roseobacter Lineage CHAB-I-5 Journal Article

In: Applied and Environmental Microbiology, vol. 82, no. 7, 2016.

Abstract | Links | BibTeX

A, Eiler; R, Mondav; L, Sinclair; L, Fernandez-Vidal; DG, Scofield; P, Schwientek; M, Martinez-Garcia; D, Torrents; KD, McMahon; SGE, Andersson; R, Stepanauskas; T, Woyke; S, Bertilsson

Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria Journal Article

In: ISME, vol. 10, pp. 1902–1914, 2016.

Abstract | Links | BibTeX

2015

A, Srivastava; KD, McMahon; R, Stepanauskas; HP, Grossart

De novo synthesis and functional analysis of the phosphatase-encoding gene acI-B of uncultured Actinobacteria from Lake Stechlin (NE Germany) Journal Article

In: International Microbiology, vol. 19, no. 39-47, 2015.

Abstract | Links | BibTeX

DK, Ngugi; J, Blom; R, Stepanauskas; U, Stingl

Diversification and niche adaptations of Nitrospina-like bacteria in the polyextreme interfaces of Red Sea brines Journal Article

In: ISME, vol. 10, pp. 1383–1399, 2015.

Abstract | Links | BibTeX

JH, Munson-McGee; EK, Field; M, Bateson; C, Rooney; R, Stepanauskas; MJ, Young

Nanoarchaeota, Their Sulfolobales Host, and Nanoarchaeota Virus Distribution across Yellowstone National Park Hot Springs Journal Article

In: Applied and Environmental Microbiology, 2015.

Abstract | Links | BibTeX

SA, Carr; BN, Orcutt; KW, Mandernack; JR, Spear

Abundant Atribacteria in deep marine sediment from the Adélie Basin, Antarctica Journal Article

In: Frontiers in Microbiology, 2015.

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SA, Carr; BN, Orcutt; KW, Mandernack; JR, Spear

Abundant Atribacteria in deep marine sediment from the Adélie Basin, Antarctica Journal Article

In: Frontiers in Microbiology, vol. 6, 2015.

Abstract | Links | BibTeX

JM, Labonté; EK, Field; M, Lau; D, Chivian; van Heerden E,; KE, Wommack; TL, Kieft; TC, Onstott; R, Stepanauskas

Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population Journal Article

In: Frontiers in Microbiology, 2015.

Abstract | Links | BibTeX

JM, Labonté; BK, Swan; B, Poulos; H, Luo; S, Koren; SJ, Hallam; MB, Sullivan; T, Woyke; KE, Wommack; R, Stepanauskas

Single-cell genomics-based analysis of virus–host interactions in marine surface bacterioplankton Journal Article

In: ISME, 2015.

Abstract | Links | BibTeX

R, Stepanauskas

Wiretapping into microbial interactions by single cell genomics Journal Article

In: Frontiers in Microbiology, 2015.

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J, Martijn; F, Schullz; K, Zaremba-Niedzwiedzka; J, Viklund; R, Stepanauskas; SGE, Andersson; M, Horn; L, Guy; TJG, Ettema

Single-cell genomics of a rare environmental alphaproteobacterium provides unique insights into Rickettsiaceae evolution Journal Article

In: ISME, 2015.

Abstract | Links | BibTeX

Bagby SC Paul BG, Czornyj E

Targeted diversity generation by intraterrestrial archaea and archaeal viruses Journal Article

In: Nature Communications, 2015.

Abstract | Links | BibTeX

R, Stepanauskas

Crystal Ball: Re-defining microbial diversity from its single-celled building blocks Journal Article

In: Environmental Microbiology Reports, 2015.

Links | BibTeX

2014

EK, Field; A, Sczyrba; AE, Lyman; CC, Harris; T, Woyke; R, Stepanauskas; D, Emerson

Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount Journal Article

In: ISME, 2014.

Abstract | Links | BibTeX

M, Martínez-García; F, Santos; M, Moreno-Paz; V, Parro; J, Antón

Unveiling viral–host interactions within the ‘microbial dark matter’ Journal Article

In: Nature Communications, 2014.

Abstract | Links | BibTeX

DK, Ngugi; J, Blom; I, Alam; M, Rashid; W, Ba-Alawi; G, Zhang; T, Hikmawan; Y, Guan; A, Antunes; R, Siam; H, El Dorry; V, Bajic; U, Stingl

Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea Journal Article

In: ISME, 2014.

Abstract | Links | BibTeX

NH, Youssef; C, Rinke; R, Stepanauskas; I, Farag; T, Woyke; MS, Elshahed

Insights into the metabolism, lifestyle and putative evolutionary history of the novel archaeal phylum ‘Diapherotrites’ Journal Article

In: ISME, 2014.

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M, Gomariz; M, Martinez-Garcia; F, Santos; F, Rodriguez; S, Capella-Gutierrez; T, Gabaldon; R, Rosello-Mora

From community approaches to single-cell genomics: the discovery of ubiquitous hyperhalophilic Bacteroidetes generalists Journal Article

In: ISME, 2014.

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Kashtan, Nadav; Roggensack, Sara E; Rodrigue, Sébastien; Thompson, Jessie W; Biller, Steven J; Coe, Allison; Ding, Huiming; Marttinen, Pekka; Malmstrom, Rex R; Stocker, Roman; Follows, Michael J; Stepanauskas, Ramunas; Chisholm, Sallie W

Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus Journal Article

In: Science, vol. 344, no. 6182, pp. 416-420, 2014.

Abstract | Links | BibTeX

LJ, Baker; PF, Kemp

Exploring bacteria–diatom associations using single-cell whole genome amplification Journal Article

In: Aquatic Microbial Ecology, vol. 72, pp. 73-88, 2014.

Abstract | Links | BibTeX

2013

K, Zaremba-Niedzwiedzka; J, Viklund; W, Zhao; J, Ast; A, Sczyrba; T, Woyke; KD, McMahon; S, Bertilsson; R, Stepanauskas; SGE, Andersson

Single cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade Journal Article

In: Genome Biology, vol. 14, no. R130, 2013, ISSN: 1474-760X.

Abstract | BibTeX

S, Nurk; A, Bankevich; D, Antipov; AA, Gurevich; A, Korobeynikov; A, Lapidus; AD, Prjibelski; A, Pyshkin; A, Sirotkin; Y, Sirotkin; R, Stepanauskas; SR, Clingenpeel; T, Woyke; JS, McLean; R, Lasken; G, Tesler; MA, Alekseyev; PA, Pevzner

Assembling single-cell genomes and mini-metagenomes from chimeric MDA products Journal Article

In: Journal of Computational Biology, vol. 20, pp. 714-737, 2013.

Abstract | Links | BibTeX

GM, Garrity; J, Banfield; van der Lelie N, Eisen J; T, McMahon; D, Rusch; E, Delong; MA, Moran; C, Currie; J, Furhman; S, Hallam; P, Hugenholtz; N, Moran; K, Nelson; R, Roberts; R, Stepanauskas

Prokaryotic super program advisory committee DOE joint genome institute, Walnut Creek, CA, March 27, 2012 Journal Article

In: Standards in Genomic Sciences, vol. 8, no. 3, pp. 561-570, 2013.

Abstract | Links | BibTeX

C, Rinke; P, Schwientek; A, Sczyrba; NN, Ivanova; IJ, Anderson; J-F, Cheng; A, Darling; S, Malfatti; BK, Swan; EA, Gies; JA, Dodsworth; BP, Hedlund; G, Tsiamis; SM, Sievert; W-T, Liu; JA, Eisen; S, Hallam; N, Kyrpides; R, Stepanauskas; E, Rubin; P, Hugenholtz; T, Woyke

Insights into the phylogeny and coding potential of microbial dark matter Journal Article

In: Nature, vol. 499, pp. 431-437, 2013.

Abstract | Links | BibTeX

BK, Swan; B, Tupper; A, Sczyrba; FM, Lauro; M, Martinez-Garcia; JM, Gonzalez; H, Luo; JJ, Wright; ZC, Landry; NW, Hanson; B, Thompson; NJ, Poulton; P, Schwientek; S, Gonzalez-Acinas; SJ, Giovannoni; MA, Moran; SJ, Hallam; R, Cavicchioli; T, Woyke; R, Stepanauskas

Prevalent genome streamlining and latitudinal divergence of marine bacteria in the surface ocean Journal Article

In: PNAS, vol. 110, no. 28, pp. 11463-11468, 2013.

Abstract | Links | BibTeX

KG, Lloyd; L, Schreiber; DG, Petersen; K, Kjeldsen; MA, Lever; R, Stepanauskas; M, Richter; S, Kleindienst; S, Lenk; A, Schramm; BB, Jorgensen

Predominant archaea in marine sediments degrade detrital proteins Journal Article

In: Nature, vol. 496, pp. 215-182, 2013.

Abstract | Links | BibTeX

O, Zhaxybayeva; R, Stepanauskas; NR, Mohan; RT, Papke

Cell sorting analysis of geographically separated hypersaline environments Journal Article

In: Extremophiles, vol. 17, no. 2, pp. 265-75, 2013.

Abstract | Links | BibTeX

2012

Stepanauskas, R

Single cell genomics: an individual look at microbes Journal Article

In: Current Opinion in Microbiology, vol. 15, pp. 613-620, 2012.

Abstract | Links | BibTeX

117 entries « 2 of 3 »