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Charting the Complexity of the Marine Microbiome through Single-Cell Genomics.

Pachiadaki MG, Brown JM, Brown J, Bezuidt O, Berube PM, Biller SJ, Poulton NJ, Burkart MD, La Clair JJ, Chisholm SW, Stepanauskas R.

Cell. 2019 Dec 12;179(7):1623-1635.e11. doi: 10.1016/j.cell.2019.11.017.


Publisher Correction: Marine microbial metagenomes sampled across space and time.

Biller SJ, Berube PM, Dooley K, Williams M, Satinsky BM, Hackl T, Hogle SL, Coe A, Bergauer K, Bouman HA, Browning TJ, Corte D, Hassler C, Hulston D, Jacquot JE, Maas EW, Reinthaler T, Sintes E, Yokokawa T, Chisholm SW.

Sci Data. 2019 May 21;6(1):47. doi: 10.1038/s41597-019-0054-1.


Co-culture and biogeography of Prochlorococcus and SAR11.

Becker JW, Hogle SL, Rosendo K, Chisholm SW.

ISME J. 2019 Jun;13(6):1506-1519. doi: 10.1038/s41396-019-0365-4. Epub 2019 Feb 11.


Emergence of trait variability through the lens of nitrogen assimilation in Prochlorococcus.

Berube PM, Rasmussen A, Braakman R, Stepanauskas R, Chisholm SW.

Elife. 2019 Feb 1;8. pii: e41043. doi: 10.7554/eLife.41043.


Investigating the Heterogeneous Ice Nucleation of Sea Spray Aerosols Using Prochlorococcus as a Model Source of Marine Organic Matter.

Wolf MJ, Coe A, Dove LA, Zawadowicz MA, Dooley K, Biller SJ, Zhang Y, Chisholm SW, Cziczo DJ.

Environ Sci Technol. 2019 Feb 5;53(3):1139-1149. doi: 10.1021/acs.est.8b05150. Epub 2019 Jan 11.


Marine microbial metagenomes sampled across space and time.

Biller SJ, Berube PM, Dooley K, Williams M, Satinsky BM, Hackl T, Hogle SL, Coe A, Bergauer K, Bouman HA, Browning TJ, De Corte D, Hassler C, Hulston D, Jacquot JE, Maas EW, Reinthaler T, Sintes E, Yokokawa T, Chisholm SW.

Sci Data. 2018 Sep 4;5:180176. doi: 10.1038/sdata.2018.176. Erratum in: Sci Data. 2019 May 21;6(1):47.


Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments.

Berube PM, Biller SJ, Hackl T, Hogle SL, Satinsky BM, Becker JW, Braakman R, Collins SB, Kelly L, Berta-Thompson J, Coe A, Bergauer K, Bouman HA, Browning TJ, De Corte D, Hassler C, Hulata Y, Jacquot JE, Maas EW, Reinthaler T, Sintes E, Yokokawa T, Lindell D, Stepanauskas R, Chisholm SW.

Sci Data. 2018 Sep 4;5:180154. doi: 10.1038/sdata.2018.154.


Heterotroph Interactions Alter Prochlorococcus Transcriptome Dynamics during Extended Periods of Darkness.

Biller SJ, Coe A, Roggensack SE, Chisholm SW.

mSystems. 2018 May 29;3(3). pii: e00040-18. doi: 10.1128/mSystems.00040-18. eCollection 2018 May-Jun.


Evolutionary radiation of lanthipeptides in marine cyanobacteria.

Cubillos-Ruiz A, Berta-Thompson JW, Becker JW, van der Donk WA, Chisholm SW.

Proc Natl Acad Sci U S A. 2017 Jul 3;114(27):E5424-E5433. doi: 10.1073/pnas.1700990114. Epub 2017 Jun 19.



Chisholm SW.

Curr Biol. 2017 Jun 5;27(11):R447-R448. doi: 10.1016/j.cub.2017.02.043.


Nitrogen cost minimization is promoted by structural changes in the transcriptome of N-deprived Prochlorococcus cells.

Read RW, Berube PM, Biller SJ, Neveux I, Cubillos-Ruiz A, Chisholm SW, Grzymski JJ.

ISME J. 2017 Oct;11(10):2267-2278. doi: 10.1038/ismej.2017.88. Epub 2017 Jun 6.


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

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

ISME J. 2017 Sep;11(9):1997-2011. doi: 10.1038/ismej.2017.64. Epub 2017 May 19.


Metabolic evolution and the self-organization of ecosystems.

Braakman R, Follows MJ, Chisholm SW.

Proc Natl Acad Sci U S A. 2017 Apr 11;114(15):E3091-E3100. doi: 10.1073/pnas.1619573114. Epub 2017 Mar 27.


Visualizing Adsorption of Cyanophage P-SSP7 onto Marine Prochlorococcus.

Murata K, Zhang Q, Gerardo Galaz-Montoya J, Fu C, Coleman ML, Osburne MS, Schmid MF, Sullivan MB, Chisholm SW, Chiu W.

Sci Rep. 2017 Mar 10;7:44176. doi: 10.1038/srep44176.


Direct single-cell biomass estimates for marine bacteria via Archimedes' principle.

Cermak N, Becker JW, Knudsen SM, Chisholm SW, Manalis SR, Polz MF.

ISME J. 2017 Mar;11(3):825-828. doi: 10.1038/ismej.2016.161. Epub 2016 Dec 6.


Membrane vesicles in sea water: heterogeneous DNA content and implications for viral abundance estimates.

Biller SJ, McDaniel LD, Breitbart M, Rogers E, Paul JH, Chisholm SW.

ISME J. 2017 Feb;11(2):394-404. doi: 10.1038/ismej.2016.134. Epub 2016 Nov 8.


Gene Expression Patterns during Light and Dark Infection of Prochlorococcus by Cyanophage.

Thompson LR, Zeng Q, Chisholm SW.

PLoS One. 2016 Oct 27;11(10):e0165375. doi: 10.1371/journal.pone.0165375. eCollection 2016.


Torn apart and reunited: impact of a heterotroph on the transcriptome of Prochlorococcus.

Biller SJ, Coe A, Chisholm SW.

ISME J. 2016 Dec;10(12):2831-2843. doi: 10.1038/ismej.2016.82. Epub 2016 Jun 3.


Global genetic capacity for mixotrophy in marine picocyanobacteria.

Yelton AP, Acinas SG, Sunagawa S, Bork P, Pedrós-Alió C, Chisholm SW.

ISME J. 2016 Dec;10(12):2946-2957. doi: 10.1038/ismej.2016.64. Epub 2016 May 3.


Contribution of cyanobacterial alkane production to the ocean hydrocarbon cycle.

Lea-Smith DJ, Biller SJ, Davey MP, Cotton CA, Perez Sepulveda BM, Turchyn AV, Scanlan DJ, Smith AG, Chisholm SW, Howe CJ.

Proc Natl Acad Sci U S A. 2015 Nov 3;112(44):13591-6. doi: 10.1073/pnas.1507274112. Epub 2015 Oct 5.


Draft Genome Sequence of Alteromonas macleodii Strain MIT1002, Isolated from an Enrichment Culture of the Marine Cyanobacterium Prochlorococcus.

Biller SJ, Coe A, Martin-Cuadrado AB, Chisholm SW.

Genome Announc. 2015 Aug 27;3(4). pii: e00967-15. doi: 10.1128/genomeA.00967-15.


Response of Prochlorococcus to varying CO2:O2 ratios.

Bagby SC, Chisholm SW.

ISME J. 2015 Oct;9(10):2232-45. doi: 10.1038/ismej.2015.36. Epub 2015 Apr 7.


Prochlorococcus: the structure and function of collective diversity.

Biller SJ, Berube PM, Lindell D, Chisholm SW.

Nat Rev Microbiol. 2015 Jan;13(1):13-27. doi: 10.1038/nrmicro3378. Epub 2014 Dec 1. Review.


Physiology and evolution of nitrate acquisition in Prochlorococcus.

Berube PM, Biller SJ, Kent AG, Berta-Thompson JW, Roggensack SE, Roache-Johnson KH, Ackerman M, Moore LR, Meisel JD, Sher D, Thompson LR, Campbell L, Martiny AC, Chisholm SW.

ISME J. 2015 May;9(5):1195-207. doi: 10.1038/ismej.2014.211. Epub 2014 Oct 28.


Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus.

Kashtan N, Roggensack SE, Rodrigue S, Thompson JW, Biller SJ, Coe A, Ding H, Marttinen P, Malmstrom RR, Stocker R, Follows MJ, Stepanauskas R, Chisholm SW.

Science. 2014 Apr 25;344(6182):416-20. doi: 10.1126/science.1248575.


Closely related phytoplankton species produce similar suites of dissolved organic matter.

Becker JW, Berube PM, Follett CL, Waterbury JB, Chisholm SW, Delong EF, Repeta DJ.

Front Microbiol. 2014 Mar 28;5:111. doi: 10.3389/fmicb.2014.00111. eCollection 2014.


Bacterial vesicles in marine ecosystems.

Biller SJ, Schubotz F, Roggensack SE, Thompson AW, Summons RE, Chisholm SW.

Science. 2014 Jan 10;343(6167):183-6. doi: 10.1126/science.1243457.


Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus.

Biller SJ, Berube PM, Berta-Thompson JW, Kelly L, Roggensack SE, Awad L, Roache-Johnson KH, Ding H, Giovannoni SJ, Rocap G, Moore LR, Chisholm SW.

Sci Data. 2014 Sep 30;1:140034. doi: 10.1038/sdata.2014.34. eCollection 2014.


Genetic diversity in cultured and wild marine cyanomyoviruses reveals phosphorus stress as a strong selective agent.

Kelly L, Ding H, Huang KH, Osburne MS, Chisholm SW.

ISME J. 2013 Sep;7(9):1827-41. doi: 10.1038/ismej.2013.58. Epub 2013 May 9. Erratum in: ISME J. 2013 Sep;7(9):1876.


Genomes of marine cyanopodoviruses reveal multiple origins of diversity.

Labrie SJ, Frois-Moniz K, Osburne MS, Kelly L, Roggensack SE, Sullivan MB, Gearin G, Zeng Q, Fitzgerald M, Henn MR, Chisholm SW.

Environ Microbiol. 2013 May;15(5):1356-76. doi: 10.1111/1462-2920.12053. Epub 2013 Jan 16.


Transcriptome and proteome dynamics of a light-dark synchronized bacterial cell cycle.

Waldbauer JR, Rodrigue S, Coleman ML, Chisholm SW.

PLoS One. 2012;7(8):e43432. doi: 10.1371/journal.pone.0043432. Epub 2012 Aug 29.


Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis.

Malmstrom RR, Rodrigue S, Huang KH, Kelly L, Kern SE, Thompson A, Roggensack S, Berube PM, Henn MR, Chisholm SW.

ISME J. 2013 Jan;7(1):184-98. doi: 10.1038/ismej.2012.89. Epub 2012 Aug 16.


Marine viruses exploit their host's two-component regulatory system in response to resource limitation.

Zeng Q, Chisholm SW.

Curr Biol. 2012 Jan 24;22(2):124-8. doi: 10.1016/j.cub.2011.11.055. Epub 2012 Jan 12.


The spontaneous mutation frequencies of Prochlorococcus strains are commensurate with those of other bacteria.

Osburne MS, Holmbeck BM, Coe A, Chisholm SW.

Environ Microbiol Rep. 2011 Dec;3(6):744-9. doi: 10.1111/j.1758-2229.2011.00293.x. Epub 2011 Sep 27.


ProPortal: a resource for integrated systems biology of Prochlorococcus and its phage.

Kelly L, Huang KH, Ding H, Chisholm SW.

Nucleic Acids Res. 2012 Jan;40(Database issue):D632-40. doi: 10.1093/nar/gkr1022. Epub 2011 Nov 18.


Phosphite utilization by the marine picocyanobacterium Prochlorococcus MIT9301.

Martínez A, Osburne MS, Sharma AK, DeLong EF, Chisholm SW.

Environ Microbiol. 2012 Jun;14(6):1363-77. doi: 10.1111/j.1462-2920.2011.02612.x. Epub 2011 Oct 18.


Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism.

Thompson LR, Zeng Q, Kelly L, Huang KH, Singer AU, Stubbe J, Chisholm SW.

Proc Natl Acad Sci U S A. 2011 Sep 27;108(39):E757-64. doi: 10.1073/pnas.1102164108. Epub 2011 Aug 15.


Transcriptome response of high- and low-light-adapted Prochlorococcus strains to changing iron availability.

Thompson AW, Huang K, Saito MA, Chisholm SW.

ISME J. 2011 Oct;5(10):1580-94. doi: 10.1038/ismej.2011.49. Epub 2011 May 12.


Response of Prochlorococcus ecotypes to co-culture with diverse marine bacteria.

Sher D, Thompson JW, Kashtan N, Croal L, Chisholm SW.

ISME J. 2011 Jul;5(7):1125-32. doi: 10.1038/ismej.2011.1. Epub 2011 Feb 17.


Ecosystem-specific selection pressures revealed through comparative population genomics.

Coleman ML, Chisholm SW.

Proc Natl Acad Sci U S A. 2010 Oct 26;107(43):18634-9. doi: 10.1073/pnas.1009480107. Epub 2010 Oct 11.


Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea.

McCarren J, Becker JW, Repeta DJ, Shi Y, Young CR, Malmstrom RR, Chisholm SW, DeLong EF.

Proc Natl Acad Sci U S A. 2010 Sep 21;107(38):16420-7. doi: 10.1073/pnas.1010732107. Epub 2010 Aug 31.


Unlocking short read sequencing for metagenomics.

Rodrigue S, Materna AC, Timberlake SC, Blackburn MC, Malmstrom RR, Alm EJ, Chisholm SW.

PLoS One. 2010 Jul 28;5(7):e11840. doi: 10.1371/journal.pone.0011840.


Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments.

Sullivan MB, Huang KH, Ignacio-Espinoza JC, Berlin AM, Kelly L, Weigele PR, DeFrancesco AS, Kern SE, Thompson LR, Young S, Yandava C, Fu R, Krastins B, Chase M, Sarracino D, Osburne MS, Henn MR, Chisholm SW.

Environ Microbiol. 2010 Nov;12(11):3035-56. doi: 10.1111/j.1462-2920.2010.02280.x.


Structural changes in a marine podovirus associated with release of its genome into Prochlorococcus.

Liu X, Zhang Q, Murata K, Baker ML, Sullivan MB, Fu C, Dougherty MT, Schmid MF, Osburne MS, Chisholm SW, Chiu W.

Nat Struct Mol Biol. 2010 Jul;17(7):830-6. doi: 10.1038/nsmb.1823. Epub 2010 Jun 13.


Short RNA half-lives in the slow-growing marine cyanobacterium Prochlorococcus.

Steglich C, Lindell D, Futschik M, Rector T, Steen R, Chisholm SW.

Genome Biol. 2010;11(5):R54. doi: 10.1186/gb-2010-11-5-r54. Epub 2010 May 19.


Catalytic promiscuity in the biosynthesis of cyclic peptide secondary metabolites in planktonic marine cyanobacteria.

Li B, Sher D, Kelly L, Shi Y, Huang K, Knerr PJ, Joewono I, Rusch D, Chisholm SW, van der Donk WA.

Proc Natl Acad Sci U S A. 2010 Jun 8;107(23):10430-5. doi: 10.1073/pnas.0913677107. Epub 2010 May 17.


Temporal dynamics of Prochlorococcus ecotypes in the Atlantic and Pacific oceans.

Malmstrom RR, Coe A, Kettler GC, Martiny AC, Frias-Lopez J, Zinser ER, Chisholm SW.

ISME J. 2010 Oct;4(10):1252-64. doi: 10.1038/ismej.2010.60. Epub 2010 May 13.


UV hyper-resistance in Prochlorococcus MED4 results from a single base pair deletion just upstream of an operon encoding nudix hydrolase and photolyase.

Osburne MS, Holmbeck BM, Frias-Lopez J, Steen R, Huang K, Kelly L, Coe A, Waraska K, Gagne A, Chisholm SW.

Environ Microbiol. 2010 Jul;12(7):1978-88. doi: 10.1111/j.1462-2920.2010.02203.x. Epub 2010 Mar 23.


Modeling selective pressures on phytoplankton in the global ocean.

Bragg JG, Dutkiewicz S, Jahn O, Follows MJ, Chisholm SW.

PLoS One. 2010 Mar 10;5(3):e9569. doi: 10.1371/journal.pone.0009569.


Analysis of high-throughput sequencing and annotation strategies for phage genomes.

Henn MR, Sullivan MB, Stange-Thomann N, Osburne MS, Berlin AM, Kelly L, Yandava C, Kodira C, Zeng Q, Weiand M, Sparrow T, Saif S, Giannoukos G, Young SK, Nusbaum C, Birren BW, Chisholm SW.

PLoS One. 2010 Feb 5;5(2):e9083. doi: 10.1371/journal.pone.0009083.

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