Annis Water Resource Institute - Grand Valley State University

Dick, G. J., Shriberg, M., Ogdahl, M., Alofs, K. M., Biddanda, B. A., Carrick, H., Doran, P. J., Fisk, A. T., Jones, S. E., & Klaper, R. (2025). Investing in Great Lakes Science is critical for safety and prosperity. Journal of Great Lakes Research, 102614.

Bertinetti, C., Mosley, C., Jones, S., & Torres‐Dowdall, J. (2025). Robust Sensory Traits Across Light Habitats: Visual Signals but Not Receptors Vary in Centrarchids Inhabiting Distinct Photic Environments. Molecular Ecology, 34(8), e17721. https://doi.org/10.1111/mec.17721

Oleksy, I. A., Solomon, C. T., Jones, S. E., Olson, C., Bertolet, B. L., Adrian, R., Bansal, S., Baron, J. S., Brothers, S., Chandra, S., Chou, H., Colom‐Montero, W., Culpepper, J., De Eyto, E., Farragher, M. J., Hilt, S., Holeck, K. T., Kazanjian, G., Klaus, M., … Weyhenmeyer, G. A. (2024). Controls on Lake Pelagic Primary Productivity: Formalizing the Nutrient‐Color Paradigm. Journal of Geophysical Research: Biogeosciences, 129(12), e2024JG008140. https://doi.org/10.1029/2024JG008140

Oleksy, I., Solomon, C. T., Jones, S. E., Olson, C., Bertolet, B. L., Adrian, R., Bansal, S., Baron, J. S., Brothers, S., & Chandra, S. (2024). Metabolism dataset: One year of high-frequency temperature, dissolved oxygen, wind, photosynthetically active radiation observations and low-frequency nutrient data for 58 lakes in the Global Lake Ecological Observatory Network. Environmental Data Initiative. https://par.nsf.gov/biblio/10574246

Mosley, C. L., Dassow, C. J., Solomon, C. T., & Jones, S. E. (2024). Counteracting effects of “hook avoidance” and “hook habituation” on angler catch rates in a catch‐and‐release fishery. Fisheries Management and Ecology, 31(4), e12694. https://doi.org/10.1111/fme.12694

Dassow, C., Sass, G., Shaw, S., Feiner, Z., Nieman, C., & Jones, S. (2023). Depensation in fish recruitment driven by context-dependent interactions with another predator. Fisheries Research, 262, 106675.

Kelly, P. T., & Jones, S. E. (2023). Crustacean zooplankton densities in northern temperate lakes are related to habitat temperature across a wide gradient in lake dissolved organic carbon and nutrient content. Freshwater Biology, 68(5), 767–780. https://doi.org/10.1111/fwb.14062

Solomon, C. T., Dugan, H. A., Hintz, W. D., & Jones, S. E. (2023). Upper limits for road salt pollution in lakes. Limnology and Oceanography Letters, 8(6), 859–866. https://doi.org/10.1002/lol2.10339

Bishop, C. E., Gahm, K., Hendry, A. P., Jones, S. E., Stange, M., & Solomon, C. T. (2022). Benthic–limnetic morphological variation in fishes: Dissolved organic carbon concentration produces unexpected patterns. Ecosphere, 13(3), e3965. https://doi.org/10.1002/ecs2.3965

Bertolet, B. L., Olson, C. R., Szydlowski, D. K., Solomon, C. T., & Jones, S. E. (2020). Methane and Primary Productivity in Lakes: Divergence of Temporal and Spatial Relationships. Journal of Geophysical Research: Biogeosciences, 125(9), e2020JG005864. https://doi.org/10.1029/2020JG005864

Talbot, C. J., Bolster, D., Medvigy, D., & Jones, S. E. (2022). A Terrestrial‐Aquatic Model Reveals Cross‐Scale Interactions Regulate Lateral Dissolved Organic Carbon Transport From Terrestrial Ecosystems. Journal of Geophysical Research: Biogeosciences, 127(5), e2021JG006604. https://doi.org/10.1029/2021JG006604

Vizza, C., Jones, S. E., Hart, J. A., West, W. E., & Lamberti, G. A. (2022). Pond methane dynamics, from microbial communities to ecosystem budget, during summer in Alaska. Limnology and Oceanography, 67(2), 450–467. https://doi.org/10.1002/lno.12003

Olson, C. R., & Jones, S. E. (2022). Chlorophyll–total phosphorus relationships emerge from multiscale interactions from algae to catchments. Limnology and Oceanography Letters, 7(6), 483–491. https://doi.org/10.1002/lol2.10281

Mosley, C. L., Dassow, C. J., Caffarelli, J., Ross, A. J., Sass, G. G., Shaw, S. L., Solomon, C. T., & Jones, S. E. (2022). Species differences, but not habitat, influence catch rate hyperstability across a recreational fishery landscape. Fisheries Research, 255, 106438.

Hararuk, O., Jones, S. E., & Solomon, C. T. (2022). Hydrologic Export of Soil Organic Carbon: Continental Variation and Implications. Global Biogeochemical Cycles, 36(6), e2021GB007161. https://doi.org/10.1029/2021GB007161

Oleksy, I. A., Jones, S. E., & Solomon, C. T. (2022). Hydrologic Setting Dictates the Sensitivity of Ecosystem Metabolism to Climate Variability in Lakes. Ecosystems, 25(6), 1328–1345. https://doi.org/10.1007/s10021-021-00718-5

Bertolet, B. L., Louden, S. I., & Jones, S. E. (2022). Microbial community composition, and not pH, influences lake sediment function. Ecosphere, 13(5), e4091. https://doi.org/10.1002/ecs2.4091

Oleksy, I. A., Olson, C. R., Jones, S. E., & Solomon, C. T. (2021). Hydrologic setting affects ecosystem processes. In Reference Module in Earth Systems and Environmental Sciences. Elsevier. 10.1016/B978-0-12-819166-8.00021-9

Lahne, M., Brecker, M., Jones, S. E., & Hyde, D. R. (2021). The regenerating adult zebrafish retina recapitulates developmental fate specification programs. Frontiers in Cell and Developmental Biology, 8, 617923.

Shoemaker, W. R., Jones, S. E., Muscarella, M. E., Behringer, M. G., Lehmkuhl, B. K., & Lennon, J. T. (2021). Microbial population dynamics and evolutionary outcomes under extreme energy limitation. Proceedings of the National Academy of Sciences, 118(33), e2101691118. https://doi.org/10.1073/pnas.2101691118

Hanson, Z. J., Zwart, J. A., Jones, S. E., Hamlet, A. F., & Bolster, D. (2021). Projected changes of regional lake hydrologic characteristics in response to 21st century climate change. Inland Waters, 11(3), 335–350. https://doi.org/10.1080/20442041.2021.1924538

Trudeau, A., Dassow, C. J., Iwicki, C. M., Jones, S. E., Sass, G. G., Solomon, C. T., van Poorten, B. T., & Jensen, O. P. (2021). Estimating fishing effort across the landscape: A spatially extensive approach using models to integrate multiple data sources. Fisheries Research, 233, 105768.

Ziegler, J. P., Jardine, S. L., Jones, S. E., van Poorten, B. T., Janssen, M. A., & Solomon, C. T. (2021). Investing in the commons: Transient welfare creates incentives despite open access. Ecology and Society, 26(2). https://par.nsf.gov/servlets/purl/10287735

Solomon, C. T., Dassow, C. J., Iwicki, C. M., Jensen, O. P., Jones, S. E., Sass, G. G., Trudeau, A., Van Poorten, B. T., & Whittaker, D. (2020). Frontiers in modelling social–ecological dynamics of recreational fisheries: A review and synthesis. Fish and Fisheries, 21(5), 973–991. https://doi.org/10.1111/faf.12482

Armitage, D. W., & Jones, S. E. (2020b). Coexistence barriers confine the poleward range of a globally distributed plant. Ecology Letters, 23(12), 1838–1848. https://doi.org/10.1111/ele.13612

Trentman, M. T., Tank, J. L., Jones, S. E., McMillan, S. K., & Royer, T. V. (2020). Seasonal evaluation of biotic and abiotic factors suggests phosphorus retention in constructed floodplains in three agricultural streams. Science of the Total Environment, 729, 138744.

Armitage, D. W., & Jones, S. E. (2020a). Barriers to coexistence limit the poleward range of a globally-distributed plant. bioRxiv, 2020–02.

Solomon, C. T., Dassow, C. J., Iwicki, C. M., Jensen, O. P., Jones, S. E., Sass, G. G., Trudeau, A., Van Poorten, B. T., & Whittaker, D. (2020). Frontiers in modelling social–ecological dynamics of recreational fisheries: A review and synthesis. Fish and Fisheries, 21(5), 973–991. https://doi.org/10.1111/faf.12482

Dassow, C. J., Ross, A. J., Jensen, O. P., Sass, G. G., Van Poorten, B. T., Solomon, C. T., & Jones, S. E. (2020). Experimental demonstration of catch hyperstability from habitat aggregation, not effort sorting, in a recreational fishery. Canadian Journal of Fisheries and Aquatic Sciences, 77(4), 762–769. https://doi.org/10.1139/cjfas-2019-0245

Bertolet, B. L., Koepfli, C., & Jones, S. E. (2022). Lake Sediment Methane Responses to Organic Matter are Related to Microbial Community Composition in Experimental Microcosms. Frontiers in Environmental Science, 10, 834829.

Olson, C. R., Solomon, C. T., & Jones, S. E. (2020). Shifting limitation of primary production: Experimental support for a new model in lake ecosystems. Ecology Letters, 23(12), 1800–1808. https://doi.org/10.1111/ele.13606

Locey, K. J., Muscarella, M. E., Larsen, M. L., Bray, S. R., Jones, S. E., & Lennon, J. T. (2020). Dormancy dampens the microbial distance–decay relationship. Philosophical Transactions of the Royal Society B: Biological Sciences, 375(1798), 20190243. https://doi.org/10.1098/rstb.2019.0243

Solomon, C. T., & Jones, S. E. (2020). Terrestrially Derived Dissolved Organic Matter. NALMS, Lakeline. https://www.nalms.org/wp-content/uploads/2020/04/40-1-5.pdf

Ziegler, J. P., Jones, S. E., & Solomon, C. T. (2019). Local stakeholders understand recreational fisheries as social-ecological systems but do not view governance systems as influential for system dynamics. International Journal of the Commons, 13(2), 1035–1048.

Zwart, J. A., Hararuk, O., Prairie, Y. T., Jones, S. E., & Solomon, C. T. (2019). Improving estimates and forecasts of lake carbon dynamics using data assimilation. Limnology and Oceanography: Methods, 17(2), 97–111. https://doi.org/10.1002/lom3.10302

Armitage, D. W., & Jones, S. E. (2019a). How sample heterogeneity can obscure the signal of microbial interactions. The ISME Journal, 13(11), 2639–2646.

Dassow, C. J., Jensen, O. P., Jones, S. E., Ross, A. R., Sass, G. G., van Poorten, B., & Solomon, C. T. (2019). Invisible collapse of a recreational fishery? Testing for non-linear relationship between catch and abundance of largemouth bass (Micropterus salmoides) with a whole-lake manipulation. 2019 ESA Annual Meeting (August 11–16). https://eco.confex.com/eco/2019/meetingapp.cgi/Paper/79153

Bertolet, B. L., West, W. E., Armitage, D. W., & Jones, S. E. (2019a). Methanogenesis rates related to ecosystem primary productivity and microbial community composition in temperate lake sediments. 2019 ESA Annual Meeting (August 11–16). https://eco.confex.com/eco/2019/meetingapp.cgi/Paper/78121

Bertolet, B. L., West, W. E., Armitage, D. W., & Jones, S. E. (2019b). Organic matter supply and bacterial community composition predict methanogenesis rates in temperate lake sediments. Limnology and Oceanography Letters, 4(5), 164–172. https://doi.org/10.1002/lol2.10114

Zwart, J. A., Craig, N., Kelly, P. T., Sebestyen, S. D., Solomon, C. T., Weidel, B. C., & Jones, S. E. (2016). Metabolic and physiochemical responses to a whole-lake experimental increase in dissolved organic carbon in a north-temperate lake: DOC effects on Lake Metabolism. Limnology and Oceanography, 61(2), 723–734. https://doi.org/10.1002/lno.10248

Zwart, J. A., Read, J. S., Fienen, M. N., Hamlet, A. F., Jones, S. E., & Bolster, D. (2019). Lake Biogeochemical Model Output for One Retrospective and 12 Future Climate Runs in Northern Wisconsin & Michigan, USA. US Geological Survey (USGS) Data Release, 508.

Ziegler, J. P., Dassow, C. J., Jones, S. E., Ross, A. J., & Solomon, C. T. (2019). Coarse woody habitat does not predict largemouth bass young of year mortality during the open-water season. Canadian Journal of Fisheries and Aquatic Sciences, 76(6), 998–1005. https://doi.org/10.1139/cjfas-2018-0050

Armitage, D. W., & Jones, S. E. (2019b). Negative frequency‐dependent growth underlies the stable coexistence of two cosmopolitan aquatic plants. Ecology, 100(5), e02657. https://doi.org/10.1002/ecy.2657

Hart, J. A., Vizza, C., West, W. E., Chaloner, D. T., Jones, S. E., & Lamberti, G. A. (2019). Methane Cycling Contributes to Distinct Patterns in Carbon Stable Isotopes of Wetland Detritus. Wetlands, 39(2), 361–370. https://doi.org/10.1007/s13157-018-1119-1

Maranger, R., Jones, S. E., & Cotner, J. B. (2018). Stoichiometry of carbon, nitrogen, and phosphorus through the freshwater pipe. Limnology and Oceanography Letters, 3(3), 89–101. https://doi.org/10.1002/lol2.10080

Ryan, S. F., Deines, J. M., Scriber, J. M., Pfrender, M. E., Jones, S. E., Emrich, S. J., & Hellmann, J. J. (2018). Climate-mediated hybrid zone movement revealed with genomics, museum collection, and simulation modeling. Proceedings of the National Academy of Sciences, 115(10). https://doi.org/10.1073/pnas.1714950115

Hararuk, O., Zwart, J. A., Jones, S. E., Prairie, Y., & Solomon, C. T. (2018). Model‐Data Fusion to Test Hypothesized Drivers of Lake Carbon Cycling Reveals Importance of Physical Controls. Journal of Geophysical Research: Biogeosciences, 123(3), 1130–1142. https://doi.org/10.1002/2017JG004084

Hanson, Z. J., Zwart, J. A., Vanderwall, J., Solomon, C. T., Jones, S. E., Hamlet, A. F., & Bolster, D. (2018). Integrated, Regional‐Scale Hydrologic Modeling of Inland Lakes. Journal of the American Water Resources Association, 54(6), 1302–1324. https://doi.org/10.1111/1752-1688.12688

Kelly, P. T., Solomon, C. T., Zwart, J. A., & Jones, S. E. (2018). A Framework for Understanding Variation in Pelagic Gross Primary Production of Lake Ecosystems. Ecosystems, 21(7), 1364–1376. https://doi.org/10.1007/s10021-018-0226-4

Koizumi, S., Craig, N., Zwart, J. A., Kelly, P. T., Ziegler, J. P., Weidel, B. C., Jones, S. E., & Solomon, C. T. (2018). Experimental whole-lake dissolved organic carbon increase alters fish diet and density but not growth or productivity. Canadian Journal of Fisheries and Aquatic Sciences, 75(11), 1859–1867. https://doi.org/10.1139/cjfas-2017-0283

Zwart, J. A., Hanson, Z. J., Read, J. S., Fienen, M. N., Hamlet, A. F., Bolster, D., & Jones, S. E. (2019). Cross‐Scale Interactions Dictate Regional Lake Carbon Flux and Productivity Response to Future Climate. Geophysical Research Letters, 46(15), 8840–8851. https://doi.org/10.1029/2019GL083478

Jones, S. E., Zwart, J. A., Kelly, P. T., & Solomon, C. T. (2018). Hydrologic setting constrains lake heterotrophy and terrestrial carbon fate. Limnology and Oceanography Letters, 3(3), 256–264. https://doi.org/10.1002/lol2.10054

Hall, E. K., Bernhardt, E. S., Bier, R. L., Bradford, M. A., Boot, C. M., Cotner, J. B., del Giorgio, P. A., Evans, S. E., Graham, E. B., Jones, S. E., Lennon, J. T., Locey, K. J., Nemergut, D., Osborne, B. B., Rocca, J. D., Schimel, J. P., Waldrop, M. P., & Wallenstein, M. D. (2018). Understanding how microbiomes influence the systems they inhabit. Nature Microbiology, 3(9), 977–982. https://doi.org/10.1038/s41564-018-0201-z

Vizza, C., Pechal, J. L., Benbow, M. E., Lang, J. M., Chaloner, D. T., Jones, S. E., & Lamberti, G. A. (2018). Nitrate amendment reduces biofilm biomass and shifts microbial communities in remote, oligotrophic ponds. Freshwater Science, 37(2), 251–263. https://doi.org/10.1086/697897

Crawford, J. T., Loken, L. C., West, W. E., Crary, B., Spawn, S. A., Gubbins, N., Jones, S. E., Striegl, R. G., & Stanley, E. H. (2017). Spatial heterogeneity of within‐stream methane concentrations. Journal of Geophysical Research: Biogeosciences, 122(5), 1036–1048. https://doi.org/10.1002/2016JG003698

Barberán, A., Caceres Velazquez, H., Jones, S., & Fierer, N. (2017). Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere, 2(4), e00237-17. https://doi.org/10.1128/mSphere.00237-17

Tanentzap, A. J., Kielstra, B. W., Wilkinson, G. M., Berggren, M., Craig, N., del Giorgio, P. A., Grey, J., Gunn, J. M., Jones, S. E., Karlsson, J., Solomon, C. T., & Pace, M. L. (2017). Terrestrial support of lake food webs: Synthesis reveals controls over cross-ecosystem resource use. Science Advances, 3(3), e1601765. https://doi.org/10.1126/sciadv.1601765

Locey, K. J., Lennon, J. T., Larsen, M. L., Muscarella, M. E., & Jones, S. E. (2017). Spatiotemporal effects of microbial seed banks on community structure. 2017 ESA Annual Meeting (August 6–11). https://eco.confex.com/eco/2017/meetingapp.cgi/Paper/62274

Zwart, J. A., Sebestyen, S. D., Solomon, C. T., & Jones, S. E. (2017). The Influence of Hydrologic Residence Time on Lake Carbon Cycling Dynamics Following Extreme Precipitation Events. Ecosystems, 20(5), 1000–1014. https://doi.org/10.1007/s10021-016-0088-6

Vizza, C., West, W. E., Jones, S. E., Hart, J. A., & Lamberti, G. A. (2017). Regulators of coastal wetland methane production and responses to simulated global change. Biogeosciences, 14(2), 431–446.

Weidel, B. C., Baglini, K., Jones, S. E., Kelly, P. T., Solomon, C. T., & Zwart, J. A. (2017). Light climate and dissolved organic carbon concentration influence species-specific changes in fish zooplanktivory. Inland Waters, 7(2), 210–217. https://doi.org/10.1080/20442041.2017.1329121

Vizza, C., Zwart, J. A., Jones, S. E., Tiegs, S. D., & Lamberti, G. A. (2017). Landscape patterns shape wetland pond ecosystem function from glacial headwaters to ocean. Limnology and Oceanography, 62(S1). https://doi.org/10.1002/lno.10575

Ziegler, J. P., Golebie, E. J., Jones, S. E., Weidel, B. C., & Solomon, C. T. (2017). Social‐ecological outcomes in recreational fisheries: The interaction of lakeshore development and stocking. Ecological Applications, 27(1), 56–65. https://doi.org/10.1002/eap.1433

Jones, S. E. (2017). The University of Notre Dame Environmental Research Center (UNDERC): Sixty‐Five Years of Whole‐Ecosystem Manipulations and Counting. Limnology and Oceanography Bulletin, 26(2), 38–40. https://doi.org/10.1002/lob.10178

Craig, N., Jones, S. E., Weidel, B. C., & Solomon, C. T. (2017). Life history constraints explain negative relationship between fish productivity and dissolved organic carbon in lakes. Ecology and Evolution, 7(16), 6201–6209. https://doi.org/10.1002/ece3.3108

Kelly, P. T., Weidel, B. C., Paufve, M. R., O’Malley, B. P., Watkins, J. M., Rudstam, L. G., & Jones, S. E. (2017). Concentration and biochemical gradients of seston in Lake Ontario. Journal of Great Lakes Research, 43(5), 795–803.

Zwart, J. A., Hanson, Z. J., Vanderwall, J., Bolster, D., Hamlet, A., & Jones, S. E. (2018). Spatially Explicit, Regional‐Scale Simulation of Lake Carbon Fluxes. Global Biogeochemical Cycles, 32(9), 1276–1293. https://doi.org/10.1002/2017GB005843

Godwin, S. C., Jones, S. E., Weidel, B. C., & Solomon, C. T. (2016). Erratum: Dissolved organic carbon concentration controls benthic primary production: Results from in situ chambers in north-temperate lakes. Limnology and Oceanography, 61(1), 407. https://www.jstor.org/stable/26628421

West, W. E., Creamer, K. P., & Jones, S. E. (2016). Productivity and depth regulate lake contributions to atmospheric methane. Limnology and Oceanography, 61(S1), S51–S61. https://doi.org/10.1002/lno.10247

Yoo, B., Jing, B., Jones, S. E., Lamberti, G. A., Zhu, Y., Shah, J. K., & Maginn, E. J. (2016a). Molecular mechanisms of ionic liquid cytotoxicity probed by an integrated experimental and computational approach. Scientific Reports, 6(1), 19889.

Kelly, P. T., Craig, N., Solomon, C. T., Weidel, B. C., Zwart, J. A., & Jones, S. E. (2016). Experimental whole‐lake increase of dissolved organic carbon concentration produces unexpected increase in crustacean zooplankton density. Global Change Biology, 22(8), 2766–2775. https://doi.org/10.1111/gcb.13260

Muscarella, M. E., Jones, S. E., & Lennon, J. T. (2016). Species sorting along a subsidy gradient alters bacterial community stability. Ecology, 97(8), 2034–2043. https://doi.org/10.1890/15-2026.1

Craig, N., Jones, S. E., Weidel, B. C., & Solomon, C. T. (2016). Impacts of dissolved organic carbon on productivity of fish and benthic macroinvertebrates in north temperate lakes [McGill University]. https://search.proquest.com/openview/5ad24bac974f86e39844b1c705e3d58a/1.pdf?pq-origsite=gscholar&cbl=18750&diss=y#page=39

Leff, J. W., Jones, S. E., Prober, S. M., Barberán, A., Borer, E. T., Firn, J. L., Harpole, W. S., Hobbie, S. E., Hofmockel, K. S., Knops, J. M. H., McCulley, R. L., La Pierre, K., Risch, A. C., Seabloom, E. W., Schütz, M., Steenbock, C., Stevens, C. J., & Fierer, N. (2015). Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe. Proceedings of the National Academy of Sciences, 112(35), 10967–10972. https://doi.org/10.1073/pnas.1508382112

Craig, N., Jones, S. E., Weidel, B. C., & Solomon, C. T. (2015). Habitat, not resource availability, limits consumer production in lake ecosystems—Craig—2015—- Wiley Online Library. Limnology and Oceanography. https://doi.org/10.1002/lno.10153

Solomon, C. T., Jones, S. E., Weidel, B. C., Buffam, I., Fork, M. L., Karlsson, J., Larsen, S., Lennon, J. T., Read, J. S., Sadro, S., & Saros, J. E. (2015). Ecosystem Consequences of Changing Inputs of Terrestrial Dissolved Organic Matter to Lakes: Current Knowledge and Future Challenges. Ecosystems, 18(3), 376–389. https://doi.org/10.1007/s10021-015-9848-y

Jones, S. E., & Lennon, J. T. (2010). Dormancy contributes to the maintenance of microbial diversity. Proceedings of the National Academy of Sciences, 107(13), 5881–5886. https://doi.org/10.1073/pnas.0912765107

Livermore, J. A., & Jones, S. E. (2015). Local–global overlap in diversity informs mechanisms of bacterial biogeography. The ISME Journal, 9(11), 2413–2422.

Aanderud, Z. T., Jones, S. E., Fierer, N., & Lennon, J. T. (2015). Resuscitation of the rare biosphere contributes to pulses of ecosystem activity. Frontiers in Microbiology, 6. https://doi.org/10.3389/fmicb.2015.00024

Martiny, J. B. H., Jones, S. E., & Martiny, A. C. (2015). Microbiomes in light of traits: A phylogenetic perspective. Science, 350(6261). https://doi.org/10.1126/science.aac9323

Zeng, E., Zhang, W., Emrich, S., Liu, D., Livermore, J., & Jones, S. (2015). A computational framework for integrative analysis of large microbial genomics data. 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 1109–1116. https://ieeexplore.ieee.org/abstract/document/7359837/

Docherty, K. M., Aiello, S. W., Buehler, B. K., Jones, S. E., Szymczyna, B. R., & Walker, K. A. (2015). Ionic liquid biodegradability depends on specific wastewater microbial consortia. Chemosphere, 136, 160–166.

Zwart, J. A., Solomon, C. T., & Jones, S. E. (2015). Phytoplankton traits predict ecosystem function in a global set of lakes. Ecology, 96(8), 2257–2264. https://doi.org/10.1890/14-2102.1

West, W. E., McCarthy, S. M., & Jones, S. E. (2015). Phytoplankton lipid content influences freshwater lake methanogenesis. Freshwater Biology, 60(11), 2261–2269. https://doi.org/10.1111/fwb.12652

Shade, A., Jones, S. E., Caporaso, J. G., Handelsman, J., Knight, R., Fierer, N., & Gilbert, J. A. (2014). Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity. mBio, 5(4), 10.1128/mbio.01371-14. https://doi.org/10.1128/mbio.01371-14

Godwin, S. C., Jones, S. E., Weidel, B. C., & Solomon, C. T. (2014). Dissolved organic carbon concentration controls benthic primary production: Results from in situ chambers in north‐temperate lakes. Limnology and Oceanography, 59(6), 2112–2120. https://doi.org/10.4319/lo.2014.59.6.2112

Turner, C., Barnes, M., Xu, C. C. Y., Jones, S. E., Jerde, C. L., & Lodge, D. M. (2014). Particle size distribution and optimal capture of aqueous macrobial eDNA. Methods in Ecology and Evolution, 5(7). https://doi.org/10.1111/2041-210X.12206

Zhang, W., Zeng, E., Liu, D., Jones, S. E., & Emrich, S. (2014). Mapping genomic features to functional traits through microbial whole genome sequences. International Journal of Bioinformatics Research and Applications, 10(4/5), 461. https://doi.org/10.1504/IJBRA.2014.062995

Kelly, P. T., Solomon, C. T., Weidel, B. C., & Jones, S. E. (2014). Terrestrial carbon is a resource, but not a subsidy, for lake zooplankton. Ecology, 95(5), 1236–1242. https://doi.org/10.1890/13-1586.1

Livermore, J. A., Emrich, S. J., Tan, J., & Jones, S. E. (2014). Freshwater bacterial lifestyles inferred from comparative genomics. Environmental Microbiology, 16(3), 746–758. https://doi.org/10.1111/1462-2920.12199

Zhang, W., Zeng, E., Emrich, S. J., Livermore, J., Liu, D., & Jones, S. E. (2013). Predicting bacterial functional traits from whole genome sequences using random forest. 2013 IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), 1–2. https://ieeexplore.ieee.org/abstract/document/6629212/

Lennon, J. T., Hamilton, S. K., Muscarella, M. E., Grandy, A. S., Wickings, K., & Jones, S. E. (2013). A source of terrestrial organic carbon to investigate the browning of aquatic ecosystems. PLoS One, 8(10), e75771.

Aanderud, Z. T., Jones, S. E., Schoolmaster, D. R., Fierer, N., & Lennon, J. T. (2013). Sensitivity of soil respiration and microbial communities to altered snowfall. Soil Biology and Biochemistry, 57, 217–227. https://doi.org/10.1016/j.soilbio.2012.07.022

Jennings, E., Jones, S., Arvola, L., Staehr, P. A., Gaiser, E., Jones, I. D., Weathers, K. C., Weyhenmeyer, G. A., Chiu, C.-Y., & De Eyto, E. (2012). Effects of weather-related episodic events in lakes: An analysis based on high-frequency data. Freshwater Biology, 57(3), 589–601. https://doi.org/10.1111/j.1365-2427.2011.02729.x

Jones, S. E., Solomon, C. T., & Weidel, B. C. (2012). Subsidy or Subtraction: How Do Terrestrial Inputs Influence Consumer Production in Lakes? Freshwater Reviews, 5(1), 37–49. https://doi.org/10.1608/FRJ-5.1.475

Solomon, C., Jones, S., Weidel, B., & Kelly, P. (2012, August 10). Subsidy or subtraction? Whole-lake experiments, surveys, and models to test the effects of terrestrial DOC on aquatic food webs.

Jones, S. E., Cadkin, T. A., Newton, R. J., & McMahon, K. D. (2012). Spatial and temporal scales of aquatic bacterial beta diversity. Frontiers in Microbiology, 3. https://doi.org/10.3389/fmicb.2012.00318

Burgin, A. J., Hamilton, S. K., Jones, S. E., & Lennon, J. T. (2012). Denitrification by sulfur-oxidizing bacteria in a eutrophic lake. Aquatic Microbial Ecology, 66, 283–293.

West, W. E., Coloso, J. J., & Jones, S. E. (2012). Effects of algal and terrestrial carbon on methane production rates and methanogen community structure in a temperate lake sediment. Freshwater Biology, 57(5), 949–955. https://doi.org/10.1111/j.1365-2427.2012.02755.x

Zhang, W., Zeng, E., Liu, D., Jones, S., & Emrich, S. (2012). A machine learning framework for trait based genomics. 2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), 1–6. https://ieeexplore.ieee.org/abstract/document/6182648/