@article{asamoto:2024,
  url_Paper = {2024_Asamoto_et_al.pdf},
  author = {Ciara K. Asamoto  and Yeongjun Ryu  and Kelly N. Eckartt  and Julia Kelley-Kern  and Lars E.P. Dietrich  and Daniel M. Sigman  and Sebastian H. Kopf },
  title = {Stable isotopic signature of dissimilatory nitrate reduction is robust against enzyme mutation},
  journal = {Proceedings of the National Academy of Sciences},
  volume = {121},
  number = {48},
  pages = {e2416002121},
  year = {2024},
  doi = {10.1073/pnas.2416002121},
  URL = {https://www.pnas.org/doi/abs/10.1073/pnas.2416002121},
  eprint = {https://www.pnas.org/doi/pdf/10.1073/pnas.2416002121}
}

@article{rhim:2024,
  url_Paper = {2024_Rhim_et_al.pdf},
  title = {Metabolic imprints in the hydrogen isotopes of Archaeoglobus fulgidus tetraether lipids},
  journal = {Geochimica et Cosmochimica Acta},
  year = {2024},
  issn = {0016-7037},
  doi = {https://doi.org/10.1016/j.gca.2024.09.032},
  url = {https://www.sciencedirect.com/science/article/pii/S0016703724005131},
  author = {Jeemin H. Rhim and Sebastian Kopf and Jamie McFarlin and Ashley E. Maloney and Harpreet Batther and Carolynn M. Harris and Alice Zhou and Xiahong Feng and Yuki Weber and Shelley Hoeft-McCann and Ann Pearson and William D. Leavitt},
  keywords = {Archaeal lipids, Tetraether lipids, GDGTs, Biphytanes, Hydrogen isotope, Biomarkers}
}

@article{shipley:2024,
  url_Paper = {2024_Shipley_et_al.pdf},
  doi = {10.1371/journal.pone.0295662},
  author = {Shipley, Oliver N. AND Dabrowski, Anna J. AND Bowen, Gabriel J. AND Hayden, Brian AND Pauli, Jonathan N. AND Jordan, Christopher AND Anderson, Lesleigh AND Bailey, Adriana AND Bataille, Clement P. AND Cicero, Carla AND Close, Hilary G. AND Cook, Craig AND Cook, Joseph A. AND Desai, Ankur R. AND Evaristo, Jaivime AND Filley, Tim R. AND France, Christine A. M. AND Jackson, Andrew L. AND Kim, Sora Lee AND Kopf, Sebastian AND Loisel, Julie AND Manlick, Philip J. AND McFarlin, Jamie M. AND McMeans, Bailey C. AND O’Connell, Tamsin C. AND Pilaar Birch, Suzanne E. AND Putman, Annie L. AND Semmens, Brice X. AND Stantis, Chris AND Stricker, Craig A. AND Szejner, Paul AND Trammell, Tara L. E. AND Uhen, Mark D. AND Weintraub-Leff, Samantha AND Wooller, Matthew J. AND Williams, John W. AND Yarnes, Christopher T. AND Vander Zanden, Hannah B. AND Newsome, Seth D.},
  journal = {PLOS ONE},
  publisher = {Public Library of Science},
  title = {Design, development, and implementation of IsoBank: A centralized repository for isotopic data},
  year = {2024},
  month = {09},
  volume = {19},
  url = {https://doi.org/10.1371/journal.pone.0295662},
  pages = {1-19},
  abstract = {Stable isotope data have made pivotal contributions to nearly every discipline of the physical and natural sciences. As the generation and application of stable isotope data continues to grow exponentially, so does the need for a unifying data repository to improve accessibility and promote collaborative engagement. This paper provides an overview of the design, development, and implementation of IsoBank (www.isobank.org), a community-driven initiative to create an open-access repository for stable isotope data implemented online in 2021. A central goal of IsoBank is to provide a web-accessible database supporting interdisciplinary stable isotope research and educational opportunities. To achieve this goal, we convened a multi-disciplinary group of over 40 analytical experts, stable isotope researchers, database managers, and web developers to collaboratively design the database. This paper outlines the main features of IsoBank and provides a focused description of the core metadata structure. We present plans for future database and tool development and engagement across the scientific community. These efforts will help facilitate interdisciplinary collaboration among the many users of stable isotopic data while also offering useful data resources and standardization of metadata reporting across eco-geoinformatics landscapes.},
  number = {9}
}

Stable isotope data have made pivotal contributions to nearly every discipline of the physical and natural sciences. As the generation and application of stable isotope data continues to grow exponentially, so does the need for a unifying data repository to improve accessibility and promote collaborative engagement. This paper provides an overview of the design, development, and implementation of IsoBank (www.isobank.org), a community-driven initiative to create an open-access repository for stable isotope data implemented online in 2021. A central goal of IsoBank is to provide a web-accessible database supporting interdisciplinary stable isotope research and educational opportunities. To achieve this goal, we convened a multi-disciplinary group of over 40 analytical experts, stable isotope researchers, database managers, and web developers to collaboratively design the database. This paper outlines the main features of IsoBank and provides a focused description of the core metadata structure. We present plans for future database and tool development and engagement across the scientific community. These efforts will help facilitate interdisciplinary collaboration among the many users of stable isotopic data while also offering useful data resources and standardization of metadata reporting across eco-geoinformatics landscapes.

@article{maloney:2024,
  url_Paper = {2024_Maloney_et_al.pdf},
  author = {Ashley E. Maloney  and Sebastian H. Kopf  and Zhaoyue Zhang  and Jamie McFarlin  and Daniel B. Nelson  and Andrew L. Masterson  and Xinning Zhang },
  title = {Large enrichments in fatty acid <sup>2</sup>H/<sup>1</sup>H ratios distinguish respiration from aerobic fermentation in yeast <i>Saccharomyces cerevisiae</i>},
  journal = {Proceedings of the National Academy of Sciences},
  volume = {121},
  number = {20},
  pages = {e2310771121},
  year = {2024},
  doi = {10.1073/pnas.2310771121},
  URL = {https://www.pnas.org/doi/abs/10.1073/pnas.2310771121},
  eprint = {https://www.pnas.org/doi/pdf/10.1073/pnas.2310771121}
}

@article{kantnerova:2024,
  url_Paper = {2024_Kantnerova_et_al.pdf},
  author = {Kantnerová, Kristýna and Kuhlbusch, Nils and Juchelka, Dieter and Hilkert, Andreas and Kopf, Sebastian and Neubauer, Cajetan},
  year = {2024},
  month = {04},
  pages = {},
  title = {A guide to precise measurements of isotope abundance by ESI-Orbitrap MS},
  volume = {19},
  journal = {Nature Protocols},
  doi = {10.1038/s41596-024-00981-5}
}

@article{caro:2024,
  url_Paper = {2024_Caro_et_al.pdf},
  author = {Caro, Tristan A and Kashyap, Srishti and Brown, George and Chen, Claudia and Kopf, Sebastian H and Templeton, Alexis S},
  title = "{Single-cell measurement of microbial growth rate with Raman microspectroscopy}",
  journal = {FEMS Microbiology Ecology},
  volume = {100},
  number = {9},
  pages = {fiae110},
  year = {2024},
  month = {08},
  abstract = "{Rates of microbial growth are fundamental to understanding environmental geochemistry and ecology. However, measuring the heterogeneity of microbial activity at the single-cell level, especially within complex populations and environmental matrices, remains a forefront challenge. Stable isotope probing (SIP) is a method for assessing microbial growth and involves measuring the incorporation of an isotopic label into microbial biomass. Here, we assess Raman microspectroscopy as a SIP technique, specifically focusing on the measurement of deuterium (2H), a tracer of microbial biomass production. We correlatively measured cells grown in varying concentrations of deuterated water with both Raman spectroscopy and nanoscale secondary ion mass spectrometry (nanoSIMS), generating isotopic calibrations of microbial 2H. Relative to Raman, we find that nanoSIMS measurements of 2H are subject to substantial dilution due to rapid exchange of H during sample washing. We apply our Raman-derived calibration to a numerical model of microbial growth, explicitly parameterizing the factors controlling growth rate quantification and demonstrating that Raman–SIP can sensitively measure the growth of microorganisms with doubling times ranging from hours to years. The measurement of single-cell growth with Raman spectroscopy, a rapid, nondestructive technique, represents an important step toward application of single-cell analysis into complex sample matrices or cellular assemblages.}",
  issn = {0168-6496},
  doi = {10.1093/femsec/fiae110},
  url = {https://doi.org/10.1093/femsec/fiae110},
  eprint = {https://academic.oup.com/femsec/article-pdf/100/9/fiae110/59121656/fiae110.pdf}
}

Rates of microbial growth are fundamental to understanding environmental geochemistry and ecology. However, measuring the heterogeneity of microbial activity at the single-cell level, especially within complex populations and environmental matrices, remains a forefront challenge. Stable isotope probing (SIP) is a method for assessing microbial growth and involves measuring the incorporation of an isotopic label into microbial biomass. Here, we assess Raman microspectroscopy as a SIP technique, specifically focusing on the measurement of deuterium (2H), a tracer of microbial biomass production. We correlatively measured cells grown in varying concentrations of deuterated water with both Raman spectroscopy and nanoscale secondary ion mass spectrometry (nanoSIMS), generating isotopic calibrations of microbial 2H. Relative to Raman, we find that nanoSIMS measurements of 2H are subject to substantial dilution due to rapid exchange of H during sample washing. We apply our Raman-derived calibration to a numerical model of microbial growth, explicitly parameterizing the factors controlling growth rate quantification and demonstrating that Raman–SIP can sensitively measure the growth of microorganisms with doubling times ranging from hours to years. The measurement of single-cell growth with Raman spectroscopy, a rapid, nondestructive technique, represents an important step toward application of single-cell analysis into complex sample matrices or cellular assemblages.

@article{halamka:2024,
  url_Paper = {2024_Halamka_et_al.pdf},
  AUTHOR={Halamka, Toby A.  and Garcia, Andy  and Evans, Thomas W.  and Schubert, Stephanie  and Younkin, Adam  and Hinrichs, Kai-Uwe  and Kopf, Sebastian },
  TITLE={Occurrence of ceramides in the Acidobacterium Solibacter usitatus: implications for bacterial physiology and sphingolipids in soils},
  JOURNAL={Frontiers in Geochemistry},
  VOLUME={2},
  YEAR={2024},
  URL={https://www.frontiersin.org/journals/geochemistry/articles/10.3389/fgeoc.2024.1400278},
  DOI={10.3389/fgeoc.2024.1400278},
  ISSN={2813-5962}
}

@article{harning:2024,
  url_Paper = {2024_Harning_et_al.pdf},
  AUTHOR = {Harning, D. J. and Raberg, J. H. and McFarlin, J. M. and Axford, Y. and Florian, C. R. and \'Olafsd\'ottir, K. B. and Kopf, S. and Sep\'ulveda, J. and Miller, G. H. and Geirsd\'ottir, \'A.},
  TITLE = {Spatiotemporal variation of modern lake, stream, and soil water isotopes in Iceland},
  JOURNAL = {Hydrology and Earth System Sciences},
  VOLUME = {28},
  YEAR = {2024},
  NUMBER = {18},
  PAGES = {4275--4293},
  URL = {https://hess.copernicus.org/articles/28/4275/2024/},
  DOI = {10.5194/hess-28-4275-2024}
}

@article{leavitt:2023,
  url_Paper = {2023_Leavitt_et_al.pdf},
  title = {Controls on the hydrogen isotope composition of tetraether lipids in an autotrophic ammonia-oxidizing marine archaeon},
  journal = {Geochimica et Cosmochimica Acta},
  volume = {352},
  pages = {194-210},
  year = {2023},
  issn = {0016-7037},
  doi = {https://doi.org/10.1016/j.gca.2023.04.033},
  url = {https://www.sciencedirect.com/science/article/pii/S0016703723002028},
  author = {W.D. Leavitt and S.H. Kopf and Y. Weber and B. Chiu and J.M. McFarlin and F.J. Elling and S. Hoeft-McCann and A. Pearson},
  keywords = {Archaeal lipids, GDGTs, Biphytanes, Biomarkers}
}

@article{caro:2023,
  url_Paper = {2023_Caro_et_al.pdf},
  author = {Tristan A. Caro  and Jamie McFarlin  and Sierra Jech  and Noah Fierer  and Sebastian Kopf },
  title = {Hydrogen stable isotope probing of lipids demonstrates slow rates of microbial growth in soil},
  journal = {Proceedings of the National Academy of Sciences},
  volume = {120},
  number = {16},
  pages = {e2211625120},
  year = {2023},
  doi = {10.1073/pnas.2211625120},
  URL = {https://www.pnas.org/doi/abs/10.1073/pnas.2211625120},
  eprint = {https://www.pnas.org/doi/pdf/10.1073/pnas.2211625120}
}

@article{rempfert:2023,
  url_Paper = {2023_Rempfert_et_al.pdf},
  author={Rempfert, Kaitlin R. and Nothaft, Daniel B. and Kraus, Emily A. and Asamoto, Ciara K. and Evans, R. Dave and Spear, John R. and Matter, Juerg M. and Kopf, Sebastian H. and Templeton, Alexis S.},
	title={Subsurface biogeochemical cycling of nitrogen in the actively serpentinizing Samail Ophiolite, Oman},
	journal={Frontiers in Microbiology},
	volume={14},
	year={2023},
	URL={https://www.frontiersin.org/articles/10.3389/fmicb.2023.1139633},
	doi={10.3389/fmicb.2023.1139633},
	issn={1664-302X}
}

@article{havranek:2023,
  url_Paper = {2023_Havranek_et_al.pdf},
  author = {Havranek, R. E. and Snell, K. E. and Kopf, S. H. and Davidheiser-Kroll, B. and Morris, V. and Vaughn, B.},
  title = {Lessons from and best practices for the deployment of the Soil Water Isotope Storage System},
  journal = {EGUsphere},
  volume = {2022},
  year = {2022},
  pages = {1--29},
  URL = {https://egusphere.copernicus.org/preprints/2022/egusphere-2022-1170/},
  doi = {10.5194/egusphere-2022-1170}
}

@article{boettger:2022,
  author = {Boettger, Jason D. and Neubauer, Cajetan and Kopf, Sebastian H. and Kubicki, James D.},
  title = {Microbial Denitrification: Active Site and Reaction Path Models Predict New Isotopic Fingerprints},
  journal = {ACS Earth and Space Chemistry},
  volume = {6},
  number = {11},
  pages = {2582-2594},
  year = {2022},
  doi = {10.1021/acsearthspacechem.2c00102},
  URL = {https://doi.org/10.1021/acsearthspacechem.2c00102},
  eprint = {https://doi.org/10.1021/acsearthspacechem.2c00102}
}

@article{Halamka:2022,
url_Paper = {2022_Halamka_et_al.pdf},
author = {Halamka, Toby A. and Raberg, Jonathan H. and McFarlin, Jamie M. and Younkin, Adam D. and Mulligan, Christopher and Liu, Xiao-Lei and Kopf, Sebastian H.},
title = {Production of diverse brGDGTs by Acidobacterium Solibacter usitatus in response to temperature, pH, and O2 provides a culturing perspective on brGDGT proxies and biosynthesis},
journal = {Geobiology},
volume = {n/a},
number = {n/a},
pages = {},
keywords = {Acidobacteria, brGDGTs, paleoclimate},
doi = {https://doi.org/10.1111/gbi.12525},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/gbi.12525},
year = {2022}
}

@article{Halamka:2021,
url_Paper = {2021_Halamka_et_al.pdf},
author = {Halamka, T A and McFarlin, J M and Younkin, A D and Depoy, J and Dildar, N and Kopf, S H},
doi = {http://dx.doi.org/10.7185/geochemlet.2132},
journal = {Geochemical Perspectives Letters},
pages = {36--39},
title = {{Oxygen limitation can trigger the production of branched GDGTs in culture}},
url = {http://www.geochemicalperspectivesletters.org/article2132},
volume = {19},
year = {2021}
}

@article{Fripiat:2021,
url_Paper = {2021_Fripiat_et_al.pdf},
author = {Fripiat, Fran{\c{c}}ois and Mart{\'{i}}nez-Garc{\'{i}}a, Alfredo and Marconi, Dario and Fawcett, Sarah E and Kopf, Sebastian H and Luu, Victoria H and Rafter, Patrick A and Zhang, Run and Sigman, Daniel M and Haug, Gerald H},
doi = {10.1038/s41561-021-00836-8},
issn = {1752-0908},
journal = {Nature Geoscience},
title = {{Nitrogen isotopic constraints on nutrient transport to the upper ocean}},
url = {https://doi.org/10.1038/s41561-021-00836-8},
year = {2021}
}

@article{Nothaft:2021,
url_Paper = {2021_Nothaft_et_al.pdf},
author = {Nothaft, Daniel B. and Templeton, Alexis S. and Rhim, Jeemin H. and Wang, David T. and Labidi, Jabrane and Miller, Hannah M. and Boyd, Eric S. and Matter, Juerg M. and Ono, Shuhei and Young, Edward D. and Kopf, Sebastian H. and Kelemen, Peter B. and Conrad, Mark E. and The Oman Drilling Project Science Team},
title = {Geochemical, Biological, and Clumped Isotopologue Evidence for Substantial Microbial Methane Production Under Carbon Limitation in Serpentinites of the Samail Ophiolite, Oman},
journal = {Journal of Geophysical Research: Biogeosciences},
volume = {126},
number = {10},
pages = {e2020JG006025},
keywords = {serpentinization, hydrogen, alkane, methanogenesis, methanotrophy, Methanobacterium},
doi = {https://doi.org/10.1029/2020JG006025},
url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2020JG006025},
eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2020JG006025},
note = {e2020JG006025 2020JG006025},
year = {2021}
}

@article{Boudinot:2021,
url_Paper = {2021_Boudinot_et_al.pdf},
author = {Boudinot, F. Garrett and Kopf, Sebastian and Dildar, Nadia and Sepúlveda, Julio},
title = {Carbon Cycling During Oceanic Anoxic Event 2: Compound-Specific Carbon Isotope Evidence From the Western Interior Seaway},
journal = {Paleoceanography and Paleoclimatology},
volume = {36},
number = {9},
pages = {e2021PA004287},
doi = {https://doi.org/10.1029/2021PA004287},
url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2021PA004287},
year = {2021}
}

@article{Hilkert:2021,
url_Paper = {2021_Hilkert_et_al.pdf},
author = {Hilkert, Andreas and Böhlke, John K. and Mroczkowski, Stanley J. and Fort, Kyle L. and Aizikov, Konstantin and Wang, Xingchen T. and Kopf, Sebastian H. and Neubauer, Cajetan},
title = {Exploring the Potential of Electrospray-Orbitrap for Stable Isotope Analysis Using Nitrate as a Model},
journal = {Analytical Chemistry},
volume = {93},
number = {26},
pages = {9139-9148},
year = {2021},
doi = {10.1021/acs.analchem.1c00944},
URL = {https://doi.org/10.1021/acs.analchem.1c00944}
}

@article{Raberg:2021,
url_Paper = {2021_Raberg_et_al.pdf},
author = {Raberg, J. H. and Harning, D. J. and Crump, S. E. and de Wet, G. and Blumm, A. and Kopf, S. and Geirsd\'ottir, \'A. and Miller, G. H. and Sep\'ulveda, J.},
title = {Revised fractional abundances and warm-season temperatures substantially improve brGDGT calibrations in lake sediments},
journal = {Biogeosciences},
volume = {18},
year = {2021},
number = {12},
pages = {3579--3603},
url = {https://bg.copernicus.org/articles/18/3579/2021/},
doi = {10.5194/bg-18-3579-2021}
}

@article{Kopf:2021,
url_Paper = {2021_Kopf_Davidheiser_Kocken.pdf},
author = {Kopf, Sebastian and Davidheiser-Kroll, Brett and Kocken, Ilja},
doi = {10.21105/joss.02878},
journal = {Journal of Open Source Software},
number = {61},
pages = {2878},
title = {{Isoreader: An R package to read stable isotope data files for reproducible research}},
volume = {6},
year = {2021}
}

@article{Asamoto:2021,
url_Paper = {2021_Asamoto_et_al.pdf},
author = {Asamoto, Ciara K. and Rempfert, Kaitlin R. and Luu, Victoria H. and Younkin, Adam D. and Kopf, Sebastian H.},
title = {Enzyme-Specific Coupling of Oxygen and Nitrogen Isotope Fractionation of the Nap and Nar Nitrate Reductases},
journal = {Environmental Science \& Technology},
volume = {55},
number = {8},
pages = {5537-5546},
year = {2021},
doi = {10.1021/acs.est.0c07816},
url = {https://doi.org/10.1021/acs.est.0c07816}
}

@article{Lengger:2021,
url_Paper = {2021_Lengger_et_al.pdf},
author = {Lengger, Sabine K. and Weber, Yuki and Taylor, Kyle W.R. and Kopf, Sebastian H. and Berstan, Robert and Bull, Ian D. and Mayser, Jan-Peter and Leavitt, William D. and Blewett, Jerome and Pearson, Ann and Pancost, Richard D.},
title = {Determination of the δ2H values of high molecular weight lipids by high-temperature gas chromatography coupled to isotope ratio mass spectrometry},
journal = {Rapid Communications in Mass Spectrometry},
volume = {35},
number = {4},
pages = {e8983},
doi = {https://doi.org/10.1002/rcm.8983},
year = {2021}
}

@article{Bhatnagar:2020,
url_Paper = {2020_Bhatnagar_et_al.pdf},
author = {Bhatnagar, S and Cowley, E S and Kopf, S H and Pérez Castro, S and Kearney, S and Dawson, S C and Hanselmann, K and Ruff, S E},
title = {{Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom}},
journal = {Environmental Microbiome},
year = {2020},
volume = {15},
doi = {10.1186/s40793-019-0348-0}
}

@article{McRose:2019,
url_Paper = {2019_McRose_et_al.pdf},
author = {McRose, D L and Lee, A and Kopf, S H and Baars, O and Kraepiel, A M L and Sigman, Daniel and Morel, F M M and Zhang, X},
title = {{Effect of iron limitation on the isotopic composition of cellular and released fixed nitrogen in Azotobacter vinelandii}},
journal = {Geochimica Et Cosmochimica Acta},
year = {2019},
volume = {244},
pages = {12--23},
month = jan
}

@article{Silverman:2018,
url_Paper = {2018_Silverman_et_al.pdf},
author = {Silverman, Shaelyn N and Kopf, S H and Bebout, Brad M and Gordon, Richard and Som, Sanjoy M},
title = {{Morphological and isotopic changes of heterocystous cyanobacteria in response to N2 partial pressure}},
journal = {Geobiology},
year = {2019},
volume = {17},
pages = {60–75}
}

@article{Neubauer:2018b,
url_Paper = {2018_Neubauer_et_al.pdf},
author = {Neubauer, Cajetan and Kasi, Ajay S and Grahl, Nora and Sessions, A L and Kopf, S H and Kato, Roberta and Hogan, Deborah A and Newman, D K},
title = {{Refining the Application of Microbial Lipids as Tracers of Staphylococcus aureus Growth Rates in Cystic Fibrosis Sputum.}},
journal = {Journal of Bacteriology},
year = {2018},
pages = {1--32},
month = sep,
doi = {10.1128/JB.00365-18}
}

@article{Neubauer:2018a,
author = {Neubauer, Cajetan and Sessions, A L and Booth, Ian R and Bowen, Benjamin P and Kopf, S H and Newman, D K and Dalleska, Nathan F},
title = {{Towards measuring growth rates of pathogens during infections by D2O-labeling lipidomics}},
journal = {Rapid Communications in Mass Spectrometry},
year = {2018},
pages = {1--35},
month = sep
}

@article{Miller:2018,
url_Paper = {2018_Miller_et_al.pdf},
author = {Miller, Hannah M and Chaudhry, Nabil and Conrad, Mark E and Bill, Markus and Kopf, Sebastian H and Templeton, Alexis S},
title = {{Large carbon isotope variability during methanogenesis under alkaline conditions}},
journal = {Geochimica Et Cosmochimica Acta},
year = {2018},
volume = {237},
pages = {18--31},
month = sep
}

@article{Pasulka:2017bu,
url_Paper = {2017_Pasulka_et_al.pdf},
author = {Pasulka, Alexis L and Thamatrakoln, Kimberlee and Kopf, S H and Guan, Yunbin and Poulos, Bonnie and Moradian, Annie and Sweredoski, Michael J and Hess, Sonja and Sullivan, Mathew B and Bidle, Kay D and Orphan, Victoria Jeanne},
title = {{Interrogating marine virus-host interactions and elemental transfer with BONCAT and nanoSIMS-based methods}},
journal = {Environmental Microbiology},
year = {2017},
volume = {20},
number = {2},
pages = {671--692},
month = dec
}

@article{Marconi:2016,
url_Paper = {2016_Marconi_et_al.pdf},
author = {Marconi, D and Kopf, S H and Rafter, P A and Sigman, D},
title = {{Aerobic respiration along isopycnals leads to overestimation of the isotope effect of denitrification in the ocean water column.}},
journal = {Geochimica Et Cosmochimica Acta},
year = {2016},
volume = {197},
pages = {1--54}
}

@article{Kopf:2016,
url_Paper = {2016_Kopf_et_al.pdf},
author = {Kopf, S H and Sessions, AL and Cowley, Elise S and Reyes, Carmen and Van Sambeek, Lindsey and Hu, Yang and Orphan, Victoria Jeanne and Kato, Roberta and Newman, D K},
title = {{Trace incorporation of heavy water reveals slow and heterogeneous pathogen growth rates in cystic fibrosis sputum.}},
journal = {Proceedings of the National Academy of Sciences},
year = {2016},
volume = {113},
number = {2},
pages = {E110--6},
month = {jan}
}

@article{Kraemer:2015,
url_Paper = {2015_Kraemer_Kopf_Bau.pdf},
author = {Kraemer, Dennis and Kopf, S H and Bau, Michael},
title = {{Oxidative mobilization of cerium and uranium and enhanced release of "immobile" high field strength elements from igneous rocks in the presence of the biogenic siderophore desferrioxamine B}},
journal = {Geochimica Et Cosmochimica Acta},
year = {2015},
volume = {165},
number = {C},
pages = {263--279},
month = sep
}

@article{Cowley:2015,
url_Paper = {2015_Cowley_et_al.pdf},
author = {Cowley, Elise S and Kopf, S H and LaRiviere, Alejandro and Ziebis, Wiebke and Newman, D K},
title = {{Pediatric Cystic Fibrosis Sputum Can Be Chemically Dynamic, Anoxic, and Extremely Reduced Due to Hydrogen Sulfide Formation.}},
journal = {mBio},
year = {2015},
volume = {6},
number = {4},
pages = {e00767}
}

@article{Kopf:2015,
url_Paper = {2015_Kopf_et_al.pdf},
author = {Kopf, S H and McGlynn, Shawn E and Green-Saxena, Abigail and Guan, Yunbin and Newman, D K and Orphan, Victoria Jeanne},
title = {{Heavy water and 15N labelling with NanoSIMS analysis reveals growth rate-dependent metabolic heterogeneity in chemostats.}},
journal = {Environmental Microbiology},
year = {2015},
volume = {17},
number = {7},
pages = {2542--2556},
month = jul
}

@article{Kopf:2013,
url_Paper = {2013_Kopf_Henny_Newman.pdf},
author = {Kopf, S H and Henny, Cynthia and Newman, D K},
title = {{Ligand-enhanced abiotic iron oxidation and the effects of chemical versus biological iron cycling in anoxic environments.}},
journal = {Environmental Science {\&} Technology},
year = {2013},
volume = {47},
number = {6},
pages = {2602--2611},
month = mar
}

@article{Kopf:2012,
url_Paper = {2012_Kopf_Ono.pdf},
author = {Kopf, S H and Ono, Shuhei},
title = {{Sulfur mass-independent fractionation in liquid phase chemistry: UV photolysis of phenacylphenylsulfone as a case study}},
journal = {Geochimica Et Cosmochimica Acta},
year = {2012},
volume = {85},
number = {C},
pages = {160--169},
month = may
}

@incollection{Bose:2011,
author = {Bose, A and Kopf, S H and Newman, D K},
title = {{From Geocycles to Genomes and Back}},
booktitle = {Microbial Metal and Metalloid Metabolism},
year = {2011},
pages = {13--38},
publisher = {ASM Press},
address = {Washington, D.C.}
}

@article{Kopf:2011,
url_Paper = {2011_Kopf_Newman.pdf},
author = {Kopf, S H and Newman, D K},
title = {{Photomixotrophic growth of Rhodobacter capsulatus SB1003 on ferrous iron}},
journal = {Geobiology},
year = {2011},
pages = {no--no},
month = dec
}

@article{Kopf:2008,
url_Paper = {2008_Kopf_et_al.pdf},
author = {Kopf, S H and Ha-Duong, M and Hallegatte, S},
title = {{Using maps of city analogues to display and interpret climate change scenarios and their uncertainty}},
journal = {Natural Hazards And Earth System Sciences},
year = {2008},
volume = {8},
number = {4},
pages = {905--918}
}