Tully, B. J., Nelson, W. C., & Heidelberg, J. F. (2011). Metagenomic analysis of a complex marine planktonic thaumarchaeal community from the Gulf of Maine. Environmental Microbiology, 14(1), 254–267. http://doi.org/10.1111/j.1462-2920.2011.02628.x
Biddle, J. F., Sylvan, J. B., Brazelton, W. J., Tully, B. J., Edwards, K. J., Moyer, C. L., et al. (2011). Prospects for the study of evolution in the deep biosphere. Frontiers in Microbiology, 2, 285. http://doi.org/10.3389/fmicb.2011.00285
Tully, B. J., & Heidelberg, J. F. (2013). Microbial communities associated with ferromanganese nodules and the surrounding sediments. Frontiers in Microbiology, 4, 161. http://doi.org/10.3389/fmicb.2013.00161
Tully, B. J., Sachdeva, R., Heidelberg, K. B., & Heidelberg, J. F. (2014). Comparative genomics of planktonic Flavobacteriaceae from the Gulf of Maine using metagenomic data, Microbiome, 2(1), 1–14. http://doi.org/10.1186/2049-2618-2-34
Tully, B. J., Emerson, J. B., Andrade, K., Brocks, J. J., Allen, E. E., Banfield, J. F., & Heidelberg, K. B. (2015). De NovoSequences of Haloquadratum walsbyifrom Lake Tyrrell, Australia, Reveal a Variable Genomic Landscape. Archaea, 2015(4), 1–12. http://doi.org/10.1155/2015/875784
Meyer, J. L., Jaekel, U., Tully, B. J., Glazer, B. T., Wheat, C. G., Lin, H.-T., et al. (2016). A distinct and active bacterial community in cold oxygenated fluids circulating beneath the western flank of the Mid-Atlantic ridge. Scientific Reports, 6, 22541. http://doi.org/10.1038/srep22541
Tully, B. J., & Heidelberg, J. F. (2016). Potential Mechanisms for Microbial Energy Acquisition in Oxic Deep-Sea Sediments. Applied and Environmental Microbiology, 82(14), 4232–4243. http://doi.org/10.1128/AEM.01023-16
Graham, E. D., Heidelberg, J. F., & Tully, B. J. (2017). BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation. PeerJ, 5(Part B), e3035–19. http://doi.org/10.7717/peerj.3035
Tully BJ, Sachdeva R, Graham ED, Heidelberg JF. (2017) 290 metagenome-assembled genomes from the Mediterranean Sea: a resource for marine microbiology. PeerJ 5:e3558 https://doi.org/10.7717/peerj.3558
Tully BJ, Wheat CG, Glazer BT, Huber JA. (2017) A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer. The ISME Journal 12, 1-16 https://doi.org/10.1038/ismej.2017.187
Tully BJ, Graham ED, Heidelberg JF. (2018) The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans. Scientific Data 5(170203), 1-18 https://doi.org/10.1038/sdata.2017.203
Reese BK, Zinke LA, Sobol MS, LaRowe DE, Orcutt BN, Zhang X, Jaekel U, Wang F, Dittmar T, Defforey D, Tully B, Paytan A, Sylvan JB, Amend JP, Edwards KJ & Girguis P (2018) Nitrogen Cycling of Active Bacteria within Oligotrophic Sediment of the Mid-Atlantic Ridge Flank, Geomicrobiology Journal, https://doi.org/10.1080/01490451.2017.1392649
Graham ED, Heidelberg JF, Tully BJ. (2018) Potential for primary productivity in a globally-distributed bacterial phototroph. ISME J 350, 1–6 https://doi.org/10.1038/s41396-018-0091-3
Tully BJ. (2019) Metabolic diversity within the globally abundant Marine Group II Euryarchaea offers insight into ecological patterns. Nature Communications 10:271, 1–12 https://doi.org/10.1038/s41467-018-07840-4
Connor R, Brister R, Buchmann JP, Deboutte W, Edwards R, Martí-Carreras J, et al. (2019). NCBI’s Virus Discovery Hackathon: Engaging Research Communities to Identify Cloud Infrastructure Requirements. Genes, 10(9), 714–18. http://doi.org/10.3390/genes10090714
Lopez A, Albino D, Beraki S, Broomell S, Canela R, Dingmon T, Estrada S, Fernandez M, Savalia P, Nealson K, Emerson D, Barco R, Tully B, Amend J. (2019). Genome Sequence of Mariprofundus sp. Strain EBB-1, a Novel Marine Autotroph Isolated from an Iron-Sulfur Mineral. Microbiology Resource Announcements, 8(39), 1405–3. http://doi.org/10.1128/MRA.00995-19
Neely CJ, Graham ED, Tully BJ, MetaSanity: an integrated microbial genome evaluation and annotation pipeline, Bioinformatics, Volume 36, Issue 15, 1 August 2020, Pages 4341–4344, https://doi.org/10.1093/bioinformatics/btaa512
Nelson WC, Tully BJ, Mobberley JM. 2020. Biases in genome reconstruction from metagenomic data. PeerJ 8:e10119 https://doi.org/10.7717/peerj.10119
Graham, E.D., Tully, B.J. Marine Dadabacteria exhibit genome streamlining and phototrophy-driven niche partitioning. ISME J (2020). https://doi.org/10.1038/s41396-020-00834-5
Seyler, L. M., Trembath-Reichert, E., Tully, B. J. & Huber, J. A. Time-series transcriptomics from cold, oxic subseafloor crustal fluids reveals a motile, mixotrophic microbial community. ISME J (2020). https://doi.org/10.1038/s41396-020-00843-4
Martí-Carreras, J. et al. NCBI’s Virus Discovery Codeathon: Building “FIVE” — The Federated Index of Viral Experiments API Index. Viruses (2020). https://doi.org/10.3390/v12121424
Manck, L. E. et al. Petrobactin, a siderophore produced by Alteromonas, mediates community iron acquisition in the global ocean. ISME J (2021). https://doi.org/10.1038/s41396-021-01065-y
Tully, B. J. et al. The Bioinformatics Virtual Coordination Network: An Open-Source and Interactive Learning Environment. Frontiers in Education (2021). https://doi.org/10.3389/feduc.2021.711618
Defforey D, Tully BJ, Sylvan JB, Cade-Menun BJ, Kiel Reese B, Zinke L and Paytan A (2022) Potential Phosphorus Uptake Mechanisms in the Deep Sedimentary Biosphere. Front. Mar. Sci. 9:907527. doi: 10.3389/fmars.2022.907527
Anderson, R. E., Graham, E. D., Huber, J. A. & Tully, B. J. Microbial Populations Are Shaped by Dispersal and Recombination in a Low Biomass Subseafloor Habitat. Mbio e00354-22 (2022) doi:10.1128/mbio.00354-22.
Invited talk at Center for Environmental Genomics, Lewews, DE
Talk at International Society for Microbial Ecology, Seattle, WA
Talk at American Society for Microbiology, San Francisco, CA
Talk at American Geophysical Union, San Francisco, CA
Invited talk at C-DEBI Annual Meeting, Marina, CA
Talk at Ocean Sciences Meeting, New Orleans LA, USA
Invited talk at Wrigley Environmental Institute, Los Angeles, CA
Invited talk at C-DEBI Annual Meeting, Marina, CA
Talk at American Geophysical Union, San Francisco, California
Primary author at Association for the Sciences of Limnology and Oceanography, San Juan, PR
Primary author at Bigelow Laboratory for Ocean Sciences, East Boothbay, ME
Primary author at American Society for Microbiology Microbe 2019, San Francisco, CA
Primary author at AbSciCon, Bellevue, WA
Primary author at San Diego State University, San Diego, CA
Primary author at ASLO Ocean Sciences, San Diego, CA
Primary author at Scripps Institution of Oceanography, La Jolla, CA
Primary author at San Diego State University, San Diego, CA