Publications

2025

Stepanauskas R, Brown JM, Arasti S, Mai U, Gavelis G, Pachiadaki M, Bezuidt O, Munson-McGee JH, Chang T, Biller SJ, Berube PM, Mirarab S. “Net rate of lateral gene transfer in marine prokaryoplankton.” The ISME Journal wraf159 (2025). https://doi.org/10.1093/ismejo/wraf159
McNichol J, Williams NLR, Raut Y, Carlson C, Halewood ER, Turk-Kubo K, Zehr JP, Rees AP, Tarran G, Gradoville MR, Wietz M, Bienhold C, Metfies K, Torres-Valdés S, Mock T, Eggers SL, Jeffrey W, Moss J, Berube P, Biller S, Bodrossy L, Van De Kamp J, Brown M, Sow SLS, Armbrust EV, Fuhrman J. 2025. “Characterizing organisms from three domains of life with universal primers from throughout the global ocean.” Scientific Data 12:1078 (2025). https://doi.org/10.1038/s41597-025-05423-9
Biller SJ, Ryan MG, Li J, Burger A, Eppley JM, Hackl T and DeLong EF. “Distinct horizontal gene transfer potential of extracellular vesicles versus viral-like particles in marine habitats.” Nature Communications 16: 2126 (2025). https://doi.org/10.1038/s41467-025-57276-w
Behar S, Zadvornaya A, Wren E, Andreadis M, Tariq A, Tian ME, Krishna S, Keita K, Eich H, Enriquez J, Hansten Monterrozo BJ, Hyun C, Jenkins KL, Parameswar K, Top MM, Waag S, Ryan MG, Stein AM, Biller SJ. “Genomes of nine cultured microbes from two hydrologically connected freshwater sites in Wellesley, MA.” Microbial Resource Announcements 14(2): e00861-24 (2025). https://doi.org/10.1128/mra.00861-24

2024

Coe A, Braakman R, Biller SJ, Arellano A, Bliem C, Vo NN, von Emster K, Thomas E, DeMers M, Steglich C, Huisman J and Chisholm SW. “Emergence of metabolic coupling to the heterotroph Alteromonas promotes dark survival in Prochlorococcus.” ISME Communications 4(1):ycae131 (2024).
Becker JW, Pollak S, Berta-Thompson JW, Becker KW, Braakman R,Dooley K, Hackl T, Coe A, Arellano A, LeGault KN, Berube PM, Biller SJ, Cubillos-Ruiz A, Van Mooy BAS, and Chisholm SW. “Novel isolates expand the physiological diversity of Prochlorococcus and illuminate its macroevolution.” mBio e03497-23 (2024).
Stein AM and Biller SJ. “An ocean of diffusible information.” Trends in Genetics 40(3), 209-210 (2024). https://doi.org/10.1016/j.tig.2024.01.007
Flamholz ZN, Biller SJ, and Kelly L. “Large language models improve annotation of prokaryotic viral proteins.” Nature Microbiology 9, 537–549 (2024). https://doi.org/10.1038/s41564-023-01584-8
Welsh JA, …, MISEV Consortium, Théry C, Witwer KW. “Minimal information for studies of extracellular vesicles (MISEV2023): From basic to advanced approaches.” J. Extracellular Vesicles 13(2): e12404 (2024)

2023

Biller SJ, Coe A, Arellano AA, Dooley K, Silvestri SM, Gong JS, Yeager EA, Becker JW, and Chisholm SW. “Environmental and Taxonomic Drivers of Bacterial Extracellular Vesicle Production in Marine Ecosystems.” Applied and Environmental Microbiology (2023). https://doi.org/10.1128/aem.00594-23
Berta-Thompson JW, Thomas E, Cubillos-Ruiz A, Hackl T, Becker JW, Coe A, Biller SJ, Berube PM and Chisholm SW. “Draft genomes of three closely related low light-adapted Prochlorococcus.” BMC Genomic Data 24:11 (2023). https://doi.org/10.1186/s12863-022-01103-4
Fadeev E, Bastos CC, Hennenfeind JH, Biller SJ, Sher D, Wietz M and Herndl GJ. “Characterization of membrane vesicles in Alteromonas macleodii indicates potential roles in their copiotrophic lifestyle.” microLife 4 (2023): uqac025. https://doi.org/10.1093/femsml/uqac025
Hackl T, Laurenceau R, Ankenbrand MJ, Bliem C, Cariani Z, Thomas E, Dooley KD, Arellano AA, Hogle SL, Berube P, Leventhal GE, Luo E, Eppley JM, Zayed AA, Beaulaurier J, Stepanauskas R, Sullivan MB, DeLong EF, Biller SJ and Chisholm SW. “Novel integrative elements and genomic plasticity in ocean ecosystems.” Cell 186, no. 1 (2023): 47-62.e16. https://doi.org/10.1016/j.cell.2022.12.006.

2022

Wietz M, López-Pérez M, Sher D, Biller SJ, and Rodriguez-Valera F. “Microbe Profile: Alteromonas macleodii − a Widespread, Fast-Responding, ‘Interactive’ Marine Bacterium.” Microbiology 168, no. 11 (2022).
Eppley JM, Biller SJ, Luo E, Burger A, and DeLong EF. “Marine viral particles reveal an expansive repertoire of phage-parasitizing mobile elements.” Proc. Natl. Acad. Sci. 119(43): e2212722119 (2022).
Biller SJ, Lundeen RA, Hmelo LR, Becker KW, Arellano AA, Dooley K, Heal KR, Carlson LT, Van Mooy BAS, Ingalls AE and Chisholm SW. “Prochlorococcus extracellular vesicles: molecular composition and adsorption to diverse microbes.” Environmental Microbiology 24(1): 420-435 (2022).
Hogle SL, Hackl T, Bundy RM, Park J, Satinsky B, Hiltunen T, Biller S, Berube PM and Chisholm SW. “Siderophores as an iron source for picocyanobacteria in deep chlorophyll maximum layers of the oligotrophic ocean.” The ISME Journal 16, 1636–1646 (2022).
Biller SJ, Muñoz-Marin MC, Lima S, Matinha-Cardoso J, Tamagnini P and Oliveira P. “Isolation and Characterization of Cyanobacterial Extracellular Vesicles.” Journal of Visualized Experiments https://doi.org/10.3791/63481 (2022).

2021

Dow EG, Wood-Charlson EM, Biller SJ, Paustian T, Schirmer A, Sheik CS, Whitham JM, Krebs R, Goller CC, Allen B, Crockett Z, and Arkin AP. “Bioinformatic Teaching Resources – For Educators, by Educators – Using KBase, a Free, User-Friendly, Open Source Platform. Frontiers in Education 6:711535 (2021).
Coe A, Biller SJ, Thomas E, Boulias K, Bliem C, Arellano A, Dooley K, Rasmussen AN, LeGault K, O’Keefe TJ, Stover S, Greer EL and Chisholm SW. “Coping with darkness: The adaptive response of marine picocyanobacteria to repeated light energy deprivation.” Limnology and Oceanography 66: 3300-3312 (2021).
McNichol J, Berube PM, Biller SJ, and Fuhrman JA. “Evaluating and Improving Small Subunit rRNA PCR Primer Coverage for Bacteria, Archaea, and Eukaryotes Using Metagenomes from Global Ocean Surveys.” mSystems 6:e00565-21 (2021).
Gauthier AE, Chandler CE, Poli V, Gardner FM, Tekiau A, Smith R, Bonham KS, Cordes EE, Shank TM, Zanoni I, Goodlett DR, Biller SJ, Ernst RK, Rotjan RD, and Kagan JC. “Deep-sea microbes as tools to refine the rules of innate immune pattern recognition.” Science Immunology 6:57 eabe0531 (2021).

2020

Biller SJ. “Extracellular Vesicles in the Environment.” in Bacterial Membrane Vesicles: Biogenesis, Functions and Applications (Kaparakis-Liaskos M and Kufer T, Eds). Springer Publishing, 75-99 (2020).
Laurenceau R, Bliem C, Osburne MS, Becker JW, Biller SJ, Cubillos-Ruiz A, and Chisholm SW. “Toward a genetic system in the marine cyanobacterium Prochlorococcus.” Access Microbiology acmi000107 (2020).

2019

Pachiadaki MG, Brown JM, Brown J, Bezuidt O, Berube PM, Biller SJ, Poulton NJ, Burkart MD, LaClair JJ, Chisholm SW, and Stepanauskas R. “Charting the complexity of the marine microbiome through single-cell genomics.” Cell 179: 1623-1635 (2019).
Wolf, MJ, Coe A, Dove LA, Zawadowicz MA, Dooley K, Biller SJ, Zhang Y, Chisholm SW and Cziczo DJ. “Investigating the Heterogeneous Ice Nucleation of Sea Spray Aerosols Using Prochlorococcusas a Model Source of Marine Organic Matter.” Environmental Science & Technology 53: 1139-1149 (2019).

2018

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 and & Chisholm SW. “Marine microbial metagenomes sampled across space and time.” Scientific Data 5:180176 (2018).
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, and Chisholm SW. “Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments.” Scientific Data 5: 180154 (2018).
Biller SJ, Coe A, Roggensack SE, and Chisholm SW. “Heterotroph Interactions Alter Prochlorococcus Transcriptome Dynamics during Extended Periods of Darkness.” mSystems: e00040-18 (2018).

2017

Read RW, Berube PM, Biller SJ, Neveux I, Cubillos-Ruiz A, Chisholm SW and Grzymski JJ. “Nitrogen cost minimization is promoted by structural changes in the transcriptome of N-deprived Prochlorococcuscells.” The ISME Journal 11: 2267-2278 (2017).
Biller SJ, McDaniel LD, Breitbart M, Rogers E, Paul JH and Chisholm SW. “Membrane vesicles in sea water: heterogeneous DNA content and implications for viral abundance estimates.” The ISME Journal 11(2): 394-404 (2017).

2016

Biller SJ, Coe A, and Chisholm SW. 2016. “Torn apart and reunited: impact of a heterotroph on the transcriptome of Prochlorococcus.” The ISME Journal 10: 2831-2843 (2016).
Coe A.,Ghizzoni J, LeGault K, Biller SJ, Roggensack SE, and Chisholm SW. “Survival of Prochlorococcus in extended darkness.” Limnology and Oceanography 61: 1375–1388 (2016).

2015

Lea-Smith D, Biller SJ, Davey MP, Cotton CAR, Perez-Sepulveda BMP, Turchyn AV, Scanlan DJ, Smith AG, Chisholm SW and Howe C. “Contribution of cyanobacterial alkane production to the ocean hydrocarbon cycle.” Proceedings of the National Academy of Sciences 112(44): 13591-13596 (2015).
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 and Chisholm SW. “Physiology and evolution of nitrate acquisition in Prochlorococcus.” The ISME Journal9(5): 1195-207 (2015).
Biller SJ, Coe A, Martin-Cuadrado AB, and Chisholm SW. “Draft genome sequence of Alteromonas macleodii strain MIT1002, isolated from an enrichment culture of the marine cyanobacterium Prochlorococcus.” Genome Announcements 3(4): e00967-15 (2015).
Biller SJ, Berube PM, Lindell D and Chisholm SW. “Prochlorococcus: The structure and function of collective diversity.” Nature Reviews Microbiology 13: 13-27 (2015).

2014

Biller SJ, Schubotz F, Roggensack SE, Thompson AW, Summons RE and Chisholm SW. “Bacterial Vesicles in Marine Ecosystems.” Science 343: 183-186 (2014).
Kashtan N, Roggensack SE, Rodrigue S, Thompson JW, Biller SJ, Coe A, Ding H, Marttinen P, Stocker R, Follows M, Stepanauskas R and Chisholm SW. “Single cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus.” Science 344: 416-420 (2014).
Biller SJ, Berube, PM, Berta-Thompson JW, Kelly L, Roggensack SE, Awad L, Roache-Johnson KH, Ding H, Giovannoni SJ, Rocap G, Moore LR and Chisholm SW. “Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus.” Scientific Data 1:140034 (2014).

2012

Biller SJ, Mosier AC, Wells GF and Francis CA. “Global biodiversity of aquatic ammonia-oxidizing archaea is partitioned by habitat.” Frontiers in Aquatic Microbiology 3: 252 (2012).

2011

Biller SJ, Wayne KJ, Winkler ME and Burkholder WF. “The putative hydrolase YycJ (WalJ) affects the coordination of cell division with DNA replication in Bacillus subtilis and may play a conserved role in cell wall metabolism.” Journal of Bacteriology193: 896–908 (2011).

2009

Biller SJ and Burkholder WF. “The Bacillus subtilis SftA (YtpS) and SpoIIIE DNA translocases play distinct roles in growing cells to ensure faithful chromosome partitioning.” Molecular Microbiology 74(4): 790-809 (2009).

2006

Laskowski M, Biller SJ, Stanley K, Kajstura T, and Prusty R. “Expression Profiling of Auxin-Treated Arabidopsis Roots: Towards a molecular analysis of lateral root emergence.” Plant and Cell Physiology 47(6): 788-792 (2006).