Publications

109 entries « 2 of 3 »

2017

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: 9 (4), pp. 404-410, 2017.

Abstract | Links | BibTeX

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, 114 (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, 7 (41498), 2017.

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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, 7 (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, 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, 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, 7 (3), 2016.

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H, Fullerton; CL, Moyer

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

In: Applied and Environmental Microbiology, 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, 1 (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, 10 , pp. 1939–1953, 2016.

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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, 82 (7), 2016.

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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, 10 , pp. 1902–1914, 2016.

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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, 19 (39-47), 2015.

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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, 10 , pp. 1383–1399, 2015.

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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.

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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, 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, 6 , 2015.

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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.

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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.

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Bagby SC Paul BG, Czornyj E

Targeted diversity generation by intraterrestrial archaea and archaeal viruses Journal Article

In: Nature Communications, 2015.

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R, Stepanauskas

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

In: Environmental Microbiology Reports, 2015.

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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.

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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.

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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.

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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, 344 (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, 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, 14 (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, 20 , pp. 714-737, 2013.

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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, 8 (3), pp. 561-570, 2013.

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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, 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, 110 (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, 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, 17 (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, 15 , pp. 613-620, 2012.

Abstract | Links | BibTeX

LG, Garcia; KD, McMahon; M, Martinez-Garcia; A, Srivastava; A, Sczyrba; R, Stepanauskas; HP, Grossart; T, Woyke; F, Warnecke

Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton Journal Article

In: The ISME Journal, 7 , pp. 137-147, 2012.

Abstract | Links | BibTeX

M, Martinez-Garcia; DM, Brazel; BK, Swan; C, Arnosti; PSG, Chain; KG, Reitenga; G, Xie; NJ, Poulton; M, Lluesma Gomez; DED, Masland; B, Thompson; WK, Bellows; K, Ziervogel; CC, Lo; S, Ahmed; CD, Gleasner; CJ, Detter; R, Stepanauskas

Capturing single cell genomes of active polysaccharide degraders: An unexpected contribution of Verrucomicrobia Journal Article

In: PLoS ONE, 7 (4), pp. e35314, 2012.

Abstract | Links | BibTeX

2011

R, Ghai; L, Pasic; AB, Fernandez; AB, Martin-Cuadrado; CM, Mizuno; KD, McMahon; RT, Papke; R, Stepanauskas; B, Rodriguez-Brito; F, Rohwer; C, Sanchez-Porro; A, Ventosa; F, Rodriguez-Valera

New abundant microbial groups in aquatic hypersaline environments Journal Article

In: Scientific Report, 1 (135), 2011.

Abstract | Links | BibTeX

T, Woyke; A, Sczyrba; J, Lee; C, Rinke; D, Tighe; S, Clingenpeel; R, Malmstrom; R, Stepanauskas; J-F, Cheng

Decontamination of MDA Reagents for Single Cell Whole Genome Amplification Journal Article

In: PLoS ONE, 6 (10), pp. e26161, 2011.

Abstract | Links | BibTeX

M, Martinez-Garcia; DM, Brazel; N, Poulton; BK, Swan; M, Lluesma Gomez; D, Masland; ME, Sieracki; R, Stepanauskas

Unveiling in situ interactions between marine protists and bacteria through single cell sequencing Journal Article

In: The ISME Journal, 6 , pp. 703-707, 2011.

Abstract | Links | BibTeX

Engel P,; R, Stepanauskas; A, Moran N

Hidden Diversity in Honey Bee Gut Symbionts Detected by Single-Cell Genomics Journal Article

In: PLOS Genetics, 10 (9), pp. 1004596, 2011.

Abstract | Links | BibTeX

BK, Swan; M, Martinez-Garcia; CM, Preston; A, Sczyrba; T, Woyke; D, Lamy; T, Reinthaler; NJ, Poulton; D, Masland; M, Lluesma Gomez; ME, Sieracki; EF, DeLong; GJ, Herndl; R, Stepanauskas

Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean Journal Article

In: Science, 333 (6047), pp. 1296-1300, 2011.

Abstract | Links | BibTeX

J, Martinez-Martinez; N, Poulton; R, Stepanauskas; M, Sieracki; WH, Wilson

Targeted Sorting of Single Virus-Infected Cells of the Coccolithophore Emiliania huxleyi Journal Article

In: PLoS ONE, 6 (7), pp. e22520, 2011.

Abstract | Links | BibTeX

109 entries « 2 of 3 »