Publications

79 entries « 2 of 2 »

2014

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

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

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

Science, 344 (6182), pp. 416-420, 2014.

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LJ, Baker; PF, Kemp

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

Aquatic Microbial Ecology, 72 , pp. 73-88, 2014.

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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

Genome Biology, 14 (R130), 2013, ISSN: 1474-760X.

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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

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

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GM, Garrity; J, Banfield; van der N, Eisen Lelie 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

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

Nature, 499 , pp. 431-437, 2013.

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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

PNAS, 110 (28), pp. 11463-11468, 2013.

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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

Nature, 496 , pp. 215-182, 2013.

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

Cell sorting analysis of geographically separated hypersaline environments Journal Article

Extremophiles, 17 (2), pp. 265-75, 2013.

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2012

Stepanauskas, R

Single cell genomics: an individual look at microbes Journal Article

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

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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

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

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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

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

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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

Scientific Report, 1 (135), 2011.

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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

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

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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

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

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Engel P, ; R, Stepanauskas; A, Moran N

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

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

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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

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

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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

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

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

High throughput single cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton Journal Article

The ISME Journal, 6 , pp. 113-123, 2011.

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HS, Yoon; DC, Price; R, Stepanauskas; VD, Rajah; ME, Sieracki; WH, Wilson; EC, Yang; S, Duffy; D, Bhattacharya

Single-cell genomics reveals organismal interactions in uncultivated marine protists Journal Article

Science, 332 (6030), pp. 714-717, 2011.

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EJ, Fleming; AE, Langdon; M, Martinez-Garcia; R, Stepanauskas; N, Poulton; D, Masland; D, Emerson

What's new is old: resolving the identity of Leptothrix ochracea using single cell genomics, pyrosequencing and FISH Journal Article

PLoS ONE, 6 (3), pp. e17769, 2011.

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M, Hess; A, Sczyrba; R, Egan; TW, Kim; H, Chokhawala; G, Schroth; S, Luo; DS, Clark; F, Chen; T, Zhang; RI, Mackie; LA, Pennacchio; SG, Tringe; A, Visel; T, Woyke; Z, Wang; EM, Rubin

Metagenomic discovery of biomass-degrading genes and genomes from cow rumen Journal Article

Science, 331 (6016), pp. 463-467, 2011.

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2010

JL, Heywood; ME, Sieracki; W, Bellows; NJ, Poulton; R, Stepanauskas

Capturing diversity of marine heterotrophic protists: one cell at a time Journal Article

The ISME Journal, 5 , pp. 674-684, 2010.

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A, Reyes-Prieto; HS, Yoon; A, Moustafa; EC, Yang; RA, Andersen; SM, Boo; T, Nakayama; KI, Ishida; D, Bhattacharya

Differential gene retention in plastids of common recent origin Journal Article

Molecular biology and evolution, 27 (7), pp. 1530-1537, 2010.

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2009

T, Woyke; G, Xie; A, Copeland; JM, Gonzalez; C, Han; H, Kiss; J, Saw; P, Senin; C, Yang; S, Chatterji; J-F, Cheng; JA, Eisen; ME, Sieracki; R, Stepanauskas

Assembling the marine metagenome, one cell at a time Journal Article

PLoS ONE, 4 (4), pp. e5299, 2009.

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2008

T, Ishoey; T, Woyke; R, Stepanauskas; M, Novotny; RS, Lasken

Genomic sequencing of single microbial cells from environmental samples Journal Article

Current Opinion in Microbiology, 11 (3), pp. 198-204, 2008.

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2007

R, Stepanauskas; ME, Sieracki

Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time Journal Article

PNAS, 104 (21), pp. 9052-9057, 2007.

Abstract | Links | BibTeX

79 entries « 2 of 2 »