Publications

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CBIOMES members: per Simons Foundation policy publications resulting from projects supported by the Simons Foundation are required to carry a specifically worded acknowledgment.

For CBIOMES that language is:

“This work was supported by the Simons Collaboration on Computational Biogeochemical Modeling of Marine Ecosystems/CBIOMES) (Grant Id: XXXXX, Awardee Initials).”

CBIOMES grant numbers are listed here [restricted]


Published

2024

Robert J. W. Brewin, Xuerong Sun, Dirk A. Aurin, Johannes J. Viljoen, Christopher Walsh and Shubha Sathyendranath (2024), Superyachts could support satellite ocean colour validation, Frontiers in Remote Sensing, doi: 10.3389/frsen.2024.1336494

Deepa Rao, Zoltán Füssy, Margaret M. Brisbin, Matthew R. McIlvin, Dawn M. Moran, Andrew E. Allen, Michael J. Follows, Mak A. Saito (2024), Flexible B12 ecophysiology of Phaeocystis antarctica due to a fusion B12–independent methionine synthase with widespread homologues, PNAS, doi: 10.1073/pnas.2204075121

2023

Stephanie I. Anderson, Clara Fronda, Andrew D. Barton, Sophie Clayton, Tatiana A. Rynearson, Stephanie Dutkiewicz (2023), Phytoplankton thermal trait parameterization alters community structure and biogeochemical processes in a modeled ocean, Global Change Biology, doi: 10.1111/gcb.17093

Vincent Bian, Merrick Cai, Christopher Follett (2023), Understanding Opposing Predictions of Prochlorococcus in a Changing ClimateNature Communications, doi: 10.1038/s41467-023-36928-9

Leon Ćatipović, Frano Matić , Hrvoje Kalinić, Shubha Sathyendranath, Tomislav Županović, James Dingle, and Thomas Jackson (2023), CCGAN as a Tool for Satellite-Derived Chlorophyll a Concentration Gap Reconstruction, Journal of Marine Science and Engineering, doi: 10.3390/jmse11091814

Olga Carnicer, Ying-Yu Hu, Vinitha Ebenezer, Andrew J. Irwin, Zoe V. Finkel (2023), Genomic architecture constrains macromolecular allocation in dinoflagellates, Protist, doi: 10.1016/j.protis.2023.125992

Yuxuan Du, Jed A. Fuhrman & Fengzhu Sun (2023), ViralCC retrieves complete viral genomes and virus-host pairs from metagenomic Hi-C data, Nature Communications, doi: 10.1038/s41467-023-35945-y

Colette Fletcher-Hoppe, Yi-Chun Yeh, Yubin Raut, J. L. Weissman & Jed A. Fuhrman (2023), Symbiotic UCYN-A strains co-occurred with El Niño, relaxed upwelling, and varied eukaryotes over 10 years off Southern California, ISME COMMUN., doi: 10.1038/s43705-023-00268-y

Keisuke Inomura, Juan José Pierella Karlusich, Stephanie Dutkiewicz, Curtis Deutsch, Paul J. Harrison, Chris Bowler (2023), High Growth Rate of Diatoms Explained by Reduced Carbon Requirement and Low Energy Cost of Silica Deposition, Microbiology Spectrum, doi: 10.1128/spectrum.03311-22

Jonathan G. Izett, J. Paul Mattern, Andrew M. Moore, Christopher A. Edwards (2023), Evaluating Alternate Methods of 4D-Var Data Assimilation in a Coupled Hydrodynamic—Four-Component Biogeochemical Model of the California Current System, Ocean Modelling, doi: 10.1016/j.ocemod.2023.102253

Jasen R. Jacobsen, Christopher A. Edwards, Brian S. Powell, John A. Colosi,  Jerome Fiechter (2023), Nutricline adjustment by internal tidal beam generation enhances primary production in idealized numerical models, Front. Mar. Sci., doi: 10.3389/fmars.2023.1309011

Bror F. Jönsson, Christopher L. Follett, Jacob Bien, Stephanie Dutkiewicz, Sangwon Hyun, Gemma Kulk, Gael L. Forget, Christian Müller, Marie-Fanny Racault, Christopher N. Hill, Thomas Jackson, and Shubha Sathyendranath (2023), Using Probability Density Functions to Evaluate Models (PDFEM, v1.0) to compare a biogeochemical model with satellite-derived chlorophyll, Geoscientific Model Development, doi: 10.5194/gmd-16-4639-2023

Bror F. Jönsson, Gemma Kulk, Shubha Sathyendranath (2023), Review of algorithms estimating export production from satellite-derived properties, Front. Mar. Sci., doi: 10.3389/fmars.2023.1149938

Bror F. Jönsson, Joseph Salisbury, Elizabeth C. Atwood, Shubha Sathyendranath, Amala Mahadevan (2023), Dominant timescales of variability in global satellite chlorophyll and SST revealed with a MOving Standard deviation Saturation (MOSS) approach, Science Direct, doi: 10.1016/j.rse.2022.113404

Krinos, A., N. Cohen, M.J. Follows and H. Alexander (2023), Reverse engineering environmental meta-transcriptomes clarifies best practices for eukaryotic assemblyBMC Bioinformatics, doi: 10.1186/s12859-022-05121-y

Zhengke Li, Yong Zhang, Wei Li, Andrew J. Irwin, Zoe Finkel (2023), Common environmental stress responses in a model marine diatom, New Phytologist, doi: 10.1111/nph.19147

Jann Paul Mattern and Christopher A. Edwards (2023), Ensemble optimal interpolation for adjoint-free biogeochemical data assimilation, PLOS One, doi: 10.1371/journal.pone.0291039

Niall McGinty, Andrew J. Irwin, Zoe V. Finkel and Stephanie Dutkiewicz (2023), Using ecological partitions to assess zooplankton biogeography and seasonality, Front. Mar. Res., doi: 10.3389/fmars.2023.989770

Millette, N.C. et al (2023), Mixoplankton and mixotrophy: future
research priorities, J. Plankton Reseach, doi: 10.1093/plankt/fbad020 [Stephanie Dutkiewicz]

Crispin M. Mutshinda, Aditya Mishra, Zoe V. Finkel and Andrew J. Irwin (2023), Density regulation amplifies environmentally induced population fluctuations, PeerJ, doi: 10.7717/peerj.14701

Anne Willem Omta, Elizabeth A. Heiny, Harshana Rajakaruna, David Talmy, Michael J. Follows (2023), Trophic model closure influences ecosystem response to enrichment, Ecological Modelling, doi: 10.1016/j.ecolmodel.2022.110183

Ryan Reynolds, Sangwon Hyun, Benjamin Tully, Jacob Bien, Naomi M. Levine (2023), Identification of microbial metabolic functional guilds from large genomic datasets, Front. Microbiol., doi: 10.3389/fmicb.2023.1197329

Shubha Sathyendranath, Robert J. W. Brewin, Stefano Ciavatta, Tom Jackson, Gemma Kulk, Bror Jönsson, Victor Martinez Vicente, Trevor Platt (2023), Ocean Biology Studied from Space, Surveys in Geophysics, doi: 10.1007/s10712-023-09805-9

Enrico Ser-Giacomi, Ricardo Martinez-Garcia, Stephanie Dutkiewicz, and Michael J. Follows (2023), A Lagrangian model for drifting ecosystems reveals heterogeneity-driven enhancement of marine plankton blooms, Nature Communications, doi: 10.1038/s41467-023-41469-2

Rosie M. Sheward, Justin D. Liefer, Andrew J. Irwin, Zoe Finkel (2023), Elemental stoichiometry of the key calcifying marine phytoplankton Emiliania huxleyi under ocean climate change: A meta-analysis, Global Change Biology, doi: 10.1111/gcb.16807

Smyth, T., D. Moffat, G. Tarran, S. Sathyendranath, F. Ribalet, J. Casey (2023), Determining drivers of phytoplankton carbon to chlorophyll ratio at Atlantic Basin scale, Frontiers in Marine Science, doi: 10.3389/fmars.2023.1191216

Maria A. Soto, Dhwani Desai, Catherine Bannon, Julie LaRoche, Erin M. Bertrand (2023), Cobalamin producers and prokaryotic consumers in the Northwest Atlantic, Environmental Microbiology, doi: 10.1111/1462-2920.16363

Sun, X., Brewin, R. J., Sathyendranath, S., Dall’Olmo, G., Airs, R., Barlow, R., Bracher, A., Brotas, V., Kheireddine, M., Lamont, T., Marañón, E., Morán, X. A. G., Raitsos, D. E., Shen, F., & Tilstone, G. H. (2023), Coupling ecological concepts with an ocean-colour model: Phytoplankton size structure, Remote Sensing of Environment, doi: 10.1016/j.rse.2022.113415

2022

Mohammad M. Amirian, Andrew J. Irwin, Zoe V. Finkel (2022), Extending the Monod Model of Microbial Growth with Memory, Frontiers in Marine Science, doi: 10.3389/fmars.2022.963734

Archibald, K., C. Laufkotter, S. Dutkiewicz, H. Moeller (2022), Thermal responses in global marine planktonic food webs mediated through temperature effects on metabolism, JGR Oceans, doi: 10.1029/2022JC018932

Alberto Baudena, Enrico Ser-Giacomi, Isabel Jalón-Rojas, François Galgani and Maria Luiza Pedrotti (2022), The streaming of plastic in the Mediterranean Sea, Nature Communications, doi: 10.1038/s41467-022-30572-5

Robert J. W. Brewin, Giorgio Dall’Olmo, John Gittings, Xuerong Sun, Priscila K. Lange, Dionysios E. Raitsos, Heather A. Bouman, Ibrahim Hoteit, Jim Aiken, Shubha Sathyendranath (2022), A Conceptual Approach to Partitioning a Vertical Profile of Phytoplankton Biomass Into Contributions From Two Communities, JGR Oceans, doi: 10.1029/2021JC018195

Gregory L. Britten (2022), Extreme value distributions describe interannual variability in the seasonal North Atlantic phytoplankton bloom, Limnology and Oceanography Letters, doi: 10.1002/lol2.10247

B.B. Cael, G.L. Britten et al (2022), Climate nonlinearities: selection, uncertainty, projections, and damages, Environmental Research Letters, doi: 10.1088/1748-9326/ac8238

Dustin Carroll et al, 2022, Attribution of space-time variability in global-ocean dissolved inorganic carbon, Global Biogeochemical Cycles, doi: 10.1029/2021GB007162 [Stephanie Dutkiewicz, Jonathan M. Lauderdale, Chris Hill, Oliver Jahn] 

John R. Casey, Rene M. Boiteau, Martin Engqvist, Zoe V. Finkel, Gang Li, Justin Liefer, Christian L. Mueller, Nathalie Munoz, and Mick Follows (2022), Basin-scale biogeography of marine phytoplankton reflects cellular-scale optimization of metabolism and physiologyScience Advances, doi: 10.1126/sciadv.abl4930

E. Dart, J.A. Fuhrman, N.A. Ahlgren (2022), Diverse Marine T4-like Cyanophage Communities Are Primarily Comprised of Low-Abundance Species Including Species with Distinct Seasonal, Persistent, Occasional, or Sporadic Dynamics, Viruses, doi: 10.3390/v15020581 (added 2023)

Ophélie Da Silva, Sakina-Dorothée Ayata, Enrico Ser-Giacomi, Jade Leconte, Eric Pelletier, Cécile Fauvelot, Mohammed-Amin Madoui, Lionel Guidi, Fabien Lombard, Lucie Bittner (2022), Genomic differentiation of three pico-phytoplankton species in the Mediterranean Sea, Environmental Microbiology, doi: 10.1111/1462-2920.16171

Colomban de Vargas et al (2022), Plankton Planet: A frugal, cooperative measure of aquatic life at the planetary scale, Front. Mar. Sci., doi: 10.3389/fmars.2022.936972 [Michael. J. Follows]

Vinitha Ebenezer, Ying-Yu Hu, Olga Carnicer, Andrew J. Irwin, Michael J. Follows, Zoe V. Finkel (2022), Elemental and macromolecular composition of the marine Chloropicophyceae, a major group of oceanic photosynthetic picoeukaryotes, Limnology and Oceanography, doi: 10.1002/lno.12013

Katja Fennel, Jann Paul Mattern, Scott C. Doney, Laurent Bopp, Andrew M. Moore, Bin Wang and Liuqian Yu (2022), Ocean biogeochemical modelling, Nature Reviews Methods Primers, doi: 10.1038/s43586-022-00154-2

Follett, Christopher L., Stephanie Durkiewicz, François Ribalet, Emily Zakem, David Caron, E. Virginia Armbrust, Michael J. Follows (2022), Trophic interactions with heterotrophic bacteria limit the range of Prochlorococcus, Proceedings National Academy of Science, doi: 10.1073/pnas.2110993118

Mukund Gupta, Richard G. Williams, Jonathan M. Lauderdale, Oliver Jahn, Christopher N. Hill, Stephanie Dutkiewicz, and Michael J. Follows (2022), A nutrient relay sustains subtropical ocean productivity, PNAS, doi: 10.1073/pnas.2206504119

Ying-Yu Hu, Andrew Irwin, Zoe Finkel (2022), Improving Quantification of Particulate Phosphorus, Limnology and Oceanography: Methods, doi: 10.1002/lom3.10517

Sangwon Hyun, Aditya Mishra, Christopher L. Follett, Bror Jonsson, Gemma Kulk, Gael Forget, Marie-Fanny Racault, Thomas Jackson, Stephanie Dutkiewicz, Christian L. Müller and Jacob Bien (2022), Ocean mover’s distance: using optimal transport for analysing oceanographic dataProceedings of the Royal Society A, doi: 10.1098/rspa.2021.0875

Keisuke Inomura, Curtis Deutsch, Oliver Jahn, Stephanie Dutkiewicz and Michael J. Follows (2022), Global patterns in marine organic matter stoichiometry driven by phytoplankton ecophysiology, Nature Geoscience, doi: 10.1038/s41561-022-01066-2

Salvador J. Jorgensen et al (2022), Emergent research and priorities for shark and ray conservation, Endangered Species Research, doi: 10.3354/esr01169 [Greg Britten]

Žarko Kovač and Shubha Sathyendranath (2022), Fragility of Marine Photosynthesis, Front. Mar. Sci., doi: 10.3389/fmars.2022.963395

Térence Legrand, Anne Chenuil, Enrico Ser-Giacomi, Sophie Arnaud-Haond, Nicolas Bierne & Vincent Rossi (2022), Spatial coalescent connectivity through multi-generation dispersal modelling predicts gene flow across marine phyla, Nature Communications, doi: 10.1038/s41467-022-33499-z

Zhengke Li, Yong Zhang, Wei Li, Andrew J Irwin, Zoe V Finkel (2022), Conservation and architecture of housekeeping genes in the model marine diatom Thalassiosira pseudonana, New Phytologist,  doi: 10.1111/nph.18039

Inès Mangolte, Marina Lévy, Stephanie Dutkiewicz, Sophie Clayton, Oliver Jahn (2022), Plankton community response to fronts: winners and losersJournal of Plankton Research, doi: 10.1093/plankt/fbac010

Maniaci, G., Brewin, R.J.W., Sathyendranath, S. (2022) Concentration and distribution of phytoplankton nitrogen and carbon in the Northwest Atlantic and Indian Ocean: A simple model with applications in satellite remote sensing, Frontiers in Marine Science, doi: 10.3389/fmars.2022.1035399

Adam C. Martiny et al (2022), Marine phytoplankton resilience may moderate oligotrophic ecosystem responses and biogeochemical feedbacks to climate change, Limnology and Oceanography, doi: 10.1002/lno.12029 [Greg Britten]

Jann Paul Mattern, Kristof Glauninger, Gregory L. Britten, John R. Casey, Sangwon Hyun, Zhen Wu, E. Virginia Armbrust, Zaid Harchaoui, Francois Ribalet (2022), A Bayesian approach to modeling phytoplankton population dynamics from size distribution time seriesPLoS Computational Biology, doi: 10.1371/journal.pcbi.1009733

Simona Meiler, Gregory L. Britten, Stephanie Dutkiewicz, Mary Rose Gradoville, Pia H. Moisander, Oliver Jahn, Michael J. Follows (2022), Constraining uncertainties of diazotroph biogeography from nifH gene abundance, Limnology and Oceanography, doi: 10.1002/lno.12036

Daniel Muratore, Angela K. Boysen, Matthew J. Harke, Kevin W. Becker, John R. Casey et al (2022), Complex marine microbial communities partition metabolism of scarce resources over the diel cycleNature Ecology & Evolution, doi: 10.1038/s41559-021-01606-w

Crispin M. Mutshinda, Aditya Mishra, Zoe V. Finkel, Claire E. Widdicombe & Andrew J. Irwin (2022), Bayesian two-part modeling of phytoplankton biomass and occurrence, Hydrobiologia, doi: 10.1007/s10750-021-04789-2

Orkney, A., Sathyendranath, S., Jackson, T., Porter, M., & Bouman, H. (2022), Atlantic inflow is the primary driver of remotely sensed autumn blooms in the Barents Sea, Marine Ecology Progress Series, doi: 10.3354/meps14201

Dalit Roth-Rosenberg, Dikla Aharonovich, Anne-Willem Omta, Michael J. Follows, Daniel Sher (2022), Dynamic macromolecular composition and high exudation rates in Prochlorococcus, Limnology and Oceanography, doi: 10.1101.828897

Sanders, R. N. C., Jones, D. C., Josey, S. A., Sinha, B., and Forget, G (2022), Causes of the 2015 North Atlantic cold anomaly in a global state estimate, Ocean Sci., doi: 10.5194/os-18-953-2022

Joseph T. Siddons, Andrew J. Irwin and Zoe V. Finkel (2022), Graphical Analysis of A Marine Plankton Community Reveals Spatial, Temporal, and Niche Structure of Sub-Communities, Front. Mar. Sci., doi: 10.3389/fmars.2022.943540

Tianqi Tang, Shengwei Hou, Jed A Fuhrman, Fengzhu Sun (2022), Phage–bacterial contig association prediction with a convolutional neural network, Bioinformatics, doi: 10.1093/bioinformatics/btac239

Ioannis Tsakalakis, Michael J. Follows, Stephanie Dutkiewicz, Christopher L. Follett, Joseph J. Vallino (2022), Diel light cycles affect phytoplankton competition in the global ocean, Global Ecology and Biogeography, doi: 10.1111/geb.13562

Wakamatsu, L., Britten, G.L., Styles, E.J., Fischer, A.M, (2022), Chlorophyll-a and Sea Surface Temperature Changes in Relation to Paralytic Shellfish Toxin Production off the East Coast of Tasmania, Australia, Remote Sens., doi: 10.3390/rs14030665

JL Weissman, Marie Peras, Tyler P. Barnum, Jed A. Fuhrman (2022), Benchmarking Community-Wide Estimates of Growth Potential from Metagenomes Using Codon Usage Statistics, mSystems, doi: 10.1128/msystems.00745-22 (added 2023)

JL Weissman, Shengwei Hou and Jed Fuhrman (2022), Using DNA to predict how fast bacteria can grow, Frontiers for Young Minds, doi: 10.3389. frym.2022.714713

Zhen Wu, Dikla Aharonovich, Dalit Roth-Rosenberg, Osnat Weissberg, Tal Luzzatto-Knaan, Angela Vogts, Luca Zoccarato, Falk Eigemann, Hans-Peter Grossart, Maren Voss, Michael J. Follows & Daniel Sher (2022), Single-cell measurements and modelling reveal substantial organic carbon acquisition by Prochlorococcus, Nature Microbiology, doi: 10.1038/s41564-022-01250-5

Zhen Wu and Gael Forget (2022), PlanktonIndividuals.jl: A GPU supported individual-based phytoplankton life cycle model, Journal of Open Source Software, doi: 10.21105/joss.04207

Zhen Wu, Jincheng Li, Yanxin Sun, Josep Peñuelas, Jilin Huang, Jordi Sardans, Qingsong Jiang, Jacques C. Finlay, Gregory L. Britten, Michael J. Follows, Wei Gao, Boqiang Qin, Jinren Ni, Shouliang Huo & Yong Liu (2022), Imbalance of global nutrient cycles exacerbated by the greater retention of phosphorus over nitrogen in lakes, Nature Geosciences, doi: 10.1038/s41561-022-00958-7

Yeh, YC., Fuhrman, J.A. (2022), Contrasting diversity patterns of prokaryotes and protists over time and depth at the San-Pedro Ocean Time series, ISME Commun., doi: 10.1038/s43705-022-00121-8

Yeh, Y.C. and Jed A. Fuhrman (2022), Effects of phytoplankton, viral communities, and warming on free-living and particle-associated marine prokaryotic community structure, Nature Communications, doi: 10.1038/s41467-022-35551-4 (added 2023)

2021

Mohammad D. Ashkezari, Norland R. Hagen, Michael Denholtz, Andrew Neang, Tansy C. Burns, Rhonda L. Morales, Charlotte P. Lee, Christopher N. Hill and Virginia Armbrust (2021), Simons Collaborative Marine Atlas Project (Simons CMAP): an open-source portal to share, visualize and analyze ocean data, Limnology and Oceanography: Methods, doi: 10.1002/lom3.10439

Bardon, L. R., Ward, B. A., Dutkiewicz, S., & Cael, B. B. (2021), Testing the skill of a species distribution model using a 21st-century virtual ecosystemGeophysical Research Letters, doi: 10.1029/2021GL093455

Jacob Bien, Yan, X., Simpson, L., Christian L. Müller (2021), Tree-aggregated predictive modeling of microbiome data, Scientific Reports, doi: 10.1038/s41598-021-93645-3

Brewin, R.J.W., Sathyendranath, S., Platt, T., Bouman, H, Ciavatta, S., Dall’Olmo, G., Dingle, J., Groom, S., Jönsson, B., Kostadinov, T.S., Kulk, G., Laine, M., Martínez-Vicente, V., Psarra, S., Raitsos, D.E., Richardson, K., Rio, M-H., Rousseaux, C.S., Salisbury, J., Shutler, J.D., Walker, P. (2021), Sensing the ocean biological carbon pump from space: A review of capabilities, concepts, research gaps and future developments, Earth-Science Reviews, doi: 10.1016/j.earscirev.2021.10360

Gregory L. Britten, Carlos M. Duarte, Boris Worm (2021), The recovery of global fish stocks remains uncertain, PNAS, doi: 10.1073/pnas.2108532118

Gregory L. Britten., Y. Mohajerani, L. Primeau, M. Aydin, C. Garcia, W. Wang, B. Pasquier, B.B. Cael, F.W. Primeau (2021), Evaluating the benefits of Bayesian hierarchical methods for analyzing heterogeneous environmental datasets: a case study of marine organic carbon fluxes, Frontiers in Environmental Science, doi: 10.3389/fenvs.2021.491636

B.B. Cael, Bisson, K., Conte, M., Duret, M. T., Follett, C., Henson, S. A., et al. (2021), Open ocean particle flux variability from surface to seafloor, Geophysical Research Letters, doi: 10.1029/2021GL092895

B.B. Cael, Emma L. Cavan, and Gregory L. Britten (2021), Reconciling the size-dependence of marine particle sinking speed, Geophysical Research Letters, doi: 10.1029/2020GL091771

B.B. Cael, Stephanie Dutkiewicz, Stephanie Henson (2021),  Abrupt shifts in 21st-century plankton communitiesScience Advances, doi: 10.1126/sciadv.abf8593

O. Carnicer, A.J. Irwin, Z.V. Finkel (2021), Traits influence dinoflagellate C:N:P, European J. Phycology, doi: 10.1080/09670262.2021.1914860

Subhendu Chakraborty, Ken H. Andersen, André W. Visser, Keisuke Inomura, Michael J. Follows & Lasse Riemann  (2021), Quantifying nitrogen fixation by heterotrophic bacteria in sinking marine particlesNature Communications, doi: 10.1038/s41467-021-23875-6

Christopher L. Follett, Stephanie Dutkiewicz, Gael Forget, B.B. Cael, Michael J. Follows (2021), Moving ecological and biogeochemical transitions across the North Pacific, Limnology and Oceanography, doi: 10.1002/lno.11763

Gael Forget (2021), IndividualDisplacements.jl: a Julia package to simulate and study particle displacements within the climate systemThe Journal of Open Source Software, doi: 10.21105/joss.02813

Kovač, Ž, Platt, T, Sathyendranath, S (2021), Sverdrup meets Lambert: analytical solution for Sverdrup’s critical depth, ICES Journal of Marine Science, doi: 10.1093/icesjms/fsab013

Stephanie A. Henson, B. B. Cael, Stephanie R. Allen, and Stephanie Dutkiewicz (2021), Future phytoplankton diversity in a changing climateNature Communications, doi: 10.1038/s41467-021-25699-w

Christopher P. Kempes,  Michael J. Follows, Hillary Smith, Heather Graham, Christopher H. House, Simon A. Levin (2021), Generalized Stoichiometry and Biogeochemistry for Astrobiological ApplicationsBulletin of Mathematical Biology, doi: 10.1007/s11538-021-00877-5

Lauderdale, J. M., & Cael, B. B. (2021), Impact of remineralization profile shape on the air-sea carbon balanceGeophysical Research Letters, doi: 10.1029/2020GL091746

Z-K. Li, Y. Zhang, Y-Y. Hu, R. Sheward, A.J. Irwin, Z.V. Finkel (2021), Dynamic photophysiological stress response of a model diatom to ten environmental stresses, J. Phycol., doi: 10.1111/jpy.13072

Long, A.M., Hou, S., Ignacio-Espinoza, J.C, and J.A. Fuhrman (2021), Benchmarking microbial growth rate predictions from metagenomes, ISME J, doi: 10.1038/s41396-020-00773-1   

Niall McGinty, Andrew D. Barton, Zoe V. Finkel, David G. Johns and Andrew J. Irwin (2021), Niche conservation in copepods between ocean basins, Ecography, doi: 10.1111/ecog.05690

Niall McGinty, A.D. Barton, N.R. Record, Z.V. Finkel, D.G. Johns, C.A. Stock, A.J. Irwin (2021),  Anthropogenic climate change impacts on copepod trait biogeography, Global Change Biology, doi: 10.1111/gcb.15499

McNichol, J., Berube, P.M., Biller, S.J., and Fuhrman, J.A. (2021) Evaluating and Improving Small Subunit rRNA PCR Primer Coverage for Bacteria, Archaea, and Eukaryotes Using Metagenomes from Global Ocean SurveysmSystems, doi: 10.1128/mSystems.00565-21

Ser Giacomi, E., A. Baudena, V. Rossi, M.J. Follows, S. Clayton, R. Vasile, C. López, and E. Hernández-García (2021), Lagrangian betweenness as a measure of bottlenecks in dynamical systems with oceanographic examplesNature Communications, doi: 10.1038/s41467-021-25155-9

Smyth, TJ, Tarran, GA, Sathyendranath, S (2021), Sub-micron picoplankton shape, orientation, and internal structure combined to preferentially amplify the forward scatter, Optics Express, doi: 10.1364/OE.413576

Weissman, Jake L, Shengwei Hou, Jed A Fuhrman (2021), Estimating maximal microbial growth rates from cultures, metagenomes, and single cells via codon usage patterns, PNAS, doi: 10.1073/pnas.2016810118

Weiyi Tang, Joan Llort, Jakob Weis, Morgane M. G. Perron, Sara Basart, Zuchuan Li, Shubha Sathyendranath, Thomas Jackson, Estrella Sanz Rodriguez, Bernadette C. Proemse, Andrew R. Bowie, Christina Schallenberg, Peter G. Strutton, Richard Matear and Nicolas Cassar (2021), Widespread phytoplankton blooms triggered by 2019–2020 Australian wildfiresNature, doi: 10.1038/s41586-021-03805-8

Zhen Wu, Stephanie Dutkiewicz, Oliver Jahn, Daniel Sher, Angelicque White, Michael J. Follows (2021), Modeling Photosynthesis and Exudation in Subtropical Oceans, Global Biogeochemical Cycles, doi: 10.1029/2021GB006941

Yi-Chun Yeh, Jesse C McNichol, David M Needham, Erin B Fichot, Jed A Fuhrman, Comprehensive single-PCR 16S and 18S rRNA community analysis validated with mock communities and denoising algorithms, Envir. Microbiol., doi: 10.1111/1462-2920.15553

Yong Zhang, Zhengke Li, Kai G. Schulz, Ying-Yu Hu, Andrew J. Irwin, Zoe V. Finkel (2021), Growth-dependent changes in elemental stoichiometry and macromolecular allocation in the coccolithophore Emiliania huxleyi under different environmental conditions, Limnology and Oceanography, doi: 10.1002/lno.11854

2020

Murat Aydin, Gregory L Britten et al (2020), Anthropogenic impacts on atmospheric carbonyl sulfide since the 19th century inferred from polar firn air and ice core measurements, Earth and Space Science Open Archive, doi: 10.1002/essoar.10503126.1

Bouman HA, Jackson T, Sathyendranath SPlatt T., (2020), Vertical structure in chlorophyll profiles: influence on primary production in the Arctic OceanPhil. Trans. R. Soc. A, doi: 10.1098/rsta.2019.0351

Wei-Jun Cai, Yuan-Yuan Xu, Richard A. Feely, Rik Wanninkhof, Bror Jönsson, Simone R. Alin, Leticia Barbero, Jessica Cross, Kumiko Azetsu-Scott, Andrea Fassbender, Brendan R. Carter, Li-Qing Jiang, Pierre Pepin, Baoshan Chen, Najid Hussain, Janet Reimer, Liang Xue, Joseph E. Salisbury, José Martín Hernández-Ayón, Chris Langdon, Qian Li, Adrienne J. Sutton, Chen-Tung A. Chen, Dwight K. Gledhill (2020), Controls on surface water carbonate chemistry along North American ocean margins, Nature Communications, doi: 10.1038/s41467-020-16530-z

John Casey and Michael J. Follows (2020), A steady-state model of microbial acclimation to substrate limitation, PLoS Computational Biology, doi: 10.1371/journal.pcbi.1008140

Carlos M. Duarte, Susana Agusti, Edward Barbier, Gregory L. Britten, Juan Carlos Castilla, Jean-Pierre Gattuso, Robinson W. Fulweiler, Terry P. Hughes, Nancy Knowlton, Catherine E. Lovelock, Heike K. Lotze, Milica Predragovic, Elvira Poloczanska, Callum Roberts & Boris Worm (2020), Rebuilding marine lifeNature, doi: 10.1038/s41586-020-2146-7

Stephanie Dutkiewicz, Philip W. Boyd, Ulf Riebesell (2020), Exploring biogeochemical and ecological redundancy in phytoplankton communities in the global ocean, Global Change Biology, doi: 10.1111/gcb.15493

Stephanie Dutkiewicz, Pedro Cermeno, Oliver Jahn, Michael J. Follows, Anna E. Hickman, Darcy A. A. Taniguchi, and Ben A. Ward (2020), Dimensions of marine phytoplankton diversity, Biogeosciences, doi: 10.5194/bg-17-609-2020

Gradoville, Mary R., Hanna Farnelid, Angelicque E. White, Kendra A. Turk-Kubo, Brittany Stewart, François Ribalet, E. Virginia Armbrust, and Jonathan P. Zehr (2020), Geographical constraints on the diversity, abundance, and activity of cyanobacterum UCYN-A and other marine diazotrophs in the North Pacific, Limnology and Oceanography, doi: 10.1002/lno11423

Keisuke Inomura, Curtis Deutsch, Takako Masuda, Ondřej Prášil, Michael J. Follows (2020), Quantitative models of nitrogen-fixing organismsComputational and Structural Biotechnology Journal, doi: 10.1016/j.csbj.2020.11.022

Keisuke Inomura, Christopher L. Follett, Takako Masuda, Meri Eichner, Ondřej Prášil and Curtis Deutsch (2020), Carbon Transfer from the Host Diatom Enables Fast Growth and High Rate of N2 Fixation by Symbiotic Heterocystous CyanobacteriaPlants, doi: 10.3390/plants9020192

Inomura, K. A-W. Omta, D. Talmy, J. Bragg, C. Deutsch, and M.J. Follows (2020), A Mechanistic Model of Macromolecular Allocation, Elemental Stoichiometry, and Growth Rate in Phytoplankton, Frontiers in Microbiology, doi: 10.3389/fmicb.2020.00086

Bror F. Jönsson, Shubha Sathyendranath, Trevor Platt (2020), Trends in winter light environment over the Arctic Ocean: a perspective from two decades of ocean‐colour data, Geophysical Research Letters, doi: 10.1029/2020GL089037

Juranek, Lauren W., Angelicque E. White, Mathilde Dugenne, Fernanda Henderikx Freitas, Stephanie Dutkiewicz, Francois Ribalet, E. Virginia Armbrust, Sara Ferron, and David M. Karl. (2020), The importance of the “middle class” to ocean net community productivity, Global Biogeochemical Cycles, doi: 10.1029/2020GB006702

Žarko Kovač, Trevor Platt, and Shubha Sathyendranath (2020), Stability and resilience in a nutrient-phytoplankton marine ecosystem model, ICES Journal of Marine Science, doi: 10.1093/icesjms/fsaa067

Gemma Kulk, Trevor Platt, James Dingle, Thomas Jackson, Bror F. Jönsson, Heather A. Bouman, Marcel Babin, Robert J. W. Brewin, Martina Doblin, Marta Estrada, Francisco G. Figueiras, Ken Furuya, Natalia González-Benítez, Hafsteinn G. Gudfinnsson, Kristinn Gudmundsson, Bangqin Huang, Tomonori Isada, Žarko Kovač, Vivian A. Lutz, Emilio Marañón, Mini Raman, Katherine Richardson, Patrick D. Rozema, Willem H. van de Poll, Valeria Segura, Gavin H. Tilstone, Julia Uitz, Virginie van Dongen-Vogels, Takashi Yoshikawa and Shubha Sathyendranath (2020), Primary Production, an Index of Climate Change in the Ocean: Satellite-Based Estimates over Two Decades, Remote Sensing,  doi: 10.3390/rs12050826

Lauderdale, J.M., G. Forget, R. Braakman, S. Dutkiewicz, and M.J. Follows (2020), Microbial feedbacks optimize ocean iron availability, Proceedings of the National Academy of Sciences, doi: 10.1073/pnas.1917277117

Mruwat, Noor, Michael C. G. Carlson, Svetlana Goldin, François Ribalet, Shay Kirzner, Yotam Hulata, Stephen J. Beckett, Dror Shitrit, Joshua S. Weitz, E. Virginia Armbrust, Debbie Lindell (2020), A single-cell polony method reveals low levels of infected Prochlorococcus in oligotrophic waters despite high cyanophage abundances, ISME J., doi: 10.1038/s41396-020-00752-6

Mutshinda. C.M., Finkel, Z.V., Widdicombe, C.E. & Irwin, A.J. (2020), A trait-based taxonomy for phytoplankton biomass modeling and prediction, Diversity, doi: 10.3390/d12080295

Crispin M. Mutshinda, Andrew J. Irwin, Mikko J. Sillanpää (2020), A Bayesian Framework for Robust Quantitative Trait Locus Mapping and Outlier Detection, The International Journal of Biostatistics, doi: 10.1515/ijb-2019-0038

A.W. Omta, D. Talmy, K. Inomura, A.J. IrwinZ.V. Finkel, D. Sher, and M.J. Follows (2020), Quantifying nutrient throughput and DOM production by algae in continuous cultureJournal of Theoretical Biology, doi: 10.1016/j.jtbi.2020.110214

Jie Ren, Kai Song, Chao Deng, Nathan A. Ahlgren, Jed A. Fuhrman, Yi Li, Xiaohui Xie, Ryan Poplin & Fengzhu Sun (2020), Identifying viruses from metagenomic data using deep learning, Quantitative Biology, doi: 10.1007/s40484-019-0187-4

Shubha Sathyendranath, Trevor Platt, Žarko Kovač, James Dingle, Thomas Jackson, Robert J. W. Brewin, Peter Franks, Emilio Marañón, Gemma Kulk, and Heather A. Bouman (2020), Reconciling models of primary production and photo-acclimation, Applied Optics, doi: 10.1364/AO.386252

Maike Sonnewald, Stephanie Dutkiewicz, Christopher Hill, Gael Forget (2020), Elucidating ecological complexity: Unsupervised learning determines global marine eco-provinces, Science Advances, doi: 10.1126/sciadv.aay4740

Joseph J. Vallino and Ioannis Tsakalakis (2020), Phytoplankton temporal strategies increase entropy production in a marine food web model, Entropy, doi: 10.3390/e22111249

Weili Wang, Jie Ren, Kujin Tang, Emily Dart, Julio Cesar Ignacio-Espinoza, Jed A. Fuhrman, Jonathan Braun, Fengzhu Sun, and Nathan A. Ahlgren (2020), A network-based integrated framework for predicting virus–prokaryote interactions, NAR Genomics and Bioinformatics, doi: 10.1093/nargab/lqaa044

Emily Zakem, Jonathan Maitland Lauderdale, Reiner Schlitzer, Michael J. Follows (2020),  A flux-based threshold for anaerobic activity in the ocean, Geophysical Research Letters, doi: 10.1029/2020GL090423

Emily J. Zakem, Martin F. Polz and Michael J. Follows (2020), Redox-informed models of global biogeochemical cyclesNature Communications, doi: 10.1038/s41467-020-19454-w

2019

Braakman, R (2019), Evolution of cellular metabolism and the rise of a globally productive biosphere, Free Radical  Biology and Medicine, doi: 10.1016/j.freeadbiomed.2019.05.004

Robert J.W. Brewin, Stefano Ciavatta, Shubha Sathyendranath, Jozef Skákala, Jorn Bruggeman, David Ford, and Trevor Platt (2019), The Influence of Temperature and Community Structure on Light Absorption by Phytoplankton in the North Atlantic, Sensors, doi: 10.3390/s19194182

Casey, J., K. Bjorkman, S. Ferron, D. Karl (2019), Size dependence of physiology and metabolism within marine picoplankton populations, Limnology and Oceanography, doi: 10.1002/lno.11153

Catherine Fiset, Andrew J. Irwin, Zoe V. Finkel (2019), The macromolecular composition of non-calcified marine microalgae, Journal of Phycology, doi: 10.1111/jpy.12913

Forget, G. and D. Ferreira (2019), Global ocean heat transport dominated by heat export from the tropical Pacific, Nature Geoscience, doi: 10.1038/s41561-019-0333-7 – view paper @ https://rdcu.be/bue5V

Frajka-Williams, et al. (2019), Atlantic Meridional Overturning Circulation: Observed transports and variability, Frontiers in Marine Science, doi: 10.3389/fmars.2019.00260 [Forget]

Frawley T.H., D.K. Briscoe, P.C. Daniel, G.L. Britten, L.B. Crowder, C.J. Robinson, W.F. Gilly (2019),  Impacts of a transition to tropical oceanic conditions on Gulf of California Jumbo Squid Dosidicus gigas, ICES Journal of Marine Science, doi: 10.1093/icesjms/fsz133

Heimbach P., Fukumori, I., Hill C.N., Ponte R., Stammer D., Wunsch C., Campin J-M., Cornuelle B., Fenty I., Forget G,  Köhl A., Mazloff M., Menemenlis D., Nguyen A., Piecuch C., Trossman D., Verdy A., Wang O., Zhang H. (2019), Putting It All Together: Adding Value to the Global Ocean and Climate Observing Systems With Complete Self-Consistent Ocean State and Parameter EstimatesFrontiers in Marine Science, doi: 10.3389/fmars.2019.00055

J. Cesar Ignacio-Espinoza, Nathan A. Ahlgren and Jed A. Fuhrman (2019), Long-term stability and Red Queen-like strain dynamics in marine virusesNature Microbiology, doi: 10.1038/s41564-019-0628-x

Keisuke Inomura, Curtis Deutsch, Samuel T. Wilson, Takako Masuda, Evelyn Lawrenz, Bučinská Lenka, Roman Sobotka, Julia M. Gauglitz, Mak A. Saito, Ondřej Prášil, Michael J. Follows (2019), Quantifying Oxygen Management and Temperature and Light Dependencies of Nitrogen Fixation by Crocosphaera watsoniiMolecular Biology and Physiology, doi: 10.1128/mSphere.00531-19

Liefer, J.D., A. Garg, M.H. Fyfe, A.J. Irwin, I. Benner, C.M. Brown, M.J. Follows, A.W. Omta, Z.V. Finkel (2019), The macromolecular basis of phytoplankton C:N:P under nitrogen starvation, Frontiers in Microbiology, doi: 10.3389/fmicb.2019.00763

C. Mutshinda, C. Widdicombe, Z.V. FinkelA.J. Irwin (2019), Bayesian inference to partition determinants of community dynamics from observational time seriesCommunity Ecology, doi:  10.1556/168.2019.20.3.4

Svetlana N. Losa, Stephanie Dutkiewicz, Martin Losch, Julia Oelker, Mariana A. Soppa, Scarlett Trimborn, Hongyan Xi, and Astrid Bracher (2019), On modeling the Southern Ocean Phytoplankton Functional TypesBiogeosciences Discussions, doi: 10.5194/bg-2019-289

Jann Paul MatternChristopher A. EdwardsChristopher N. Hill (2019), Dual number-based variational data assimilation: Constructing exact tangent linear and adjoint code from nonlinear model evaluationsPLoS One, doi: 10.1371/journal.pone.0223131

Jozef I. Nissimov, David Talmy, Liti Haramaty, Helen F. Fredricks , Ehud Zelzion, Ben Knowles, A. Murat Eren , Rebecca Vandzura, Christien P. Laber, Brittany M. Schieler, Christopher T. Johns, Kuldeep D. More, Marco J. L. Coolen, Michael J. Follows, Debashish Bhattacharya, Benjamin A. S. Van Mooy, and Kay D. Bidle (2019), Biochemical diversity of glycosphingolipid biosynthesis as a driver of Coccolithovirus competitive ecology, Environmental Microbiology, doi: 10.1111/1462-2920.14633

Memarzadeh, M, G.L. Britten, B. Worm, C. Boettiger (2019), Rebuilding global fisheries under uncertainty, Proceedings of the National Academy of Sciences, doi: 10.1073/pnas.1902657116

François Ribalet, Chris Bertiaume, Annette Hynes, Jarred Swalwell, Michael Carlson,  Sophie Clayton, Gwenn Hennon, Camille Poirier, Eric Shimabukuro, Angelicque White, E. Virginia Armbrust (2019), SeaFlow data v1, high-resolution abundance, size and biomass of small phytoplankton in the North Pacific, Scientific Data, doi: 10.1038/s41597-019-0292-2

Roemmich, et al. On the future of Argo: An enhanced global array of physical and biogeochemical sensing floatsFrontiers in Marine Science, doi: 10.3389/fmars.2019.00439 [Forget]

Salgado-Hernanz, P.M., M.-F. Racault, J.S. Font-Muñoz, G. Basterretxea (2019), Trends in phytoplankton phenology in the Mediterranean Sea based on ocean-colour remote sensingRemote Sensing of Environment, doi: 10.1016/j.rse.2018.10.036

T. J. Smyth, G. A. Tarran, and S. Sathyendranath (2019), Marine picoplankton size distribution and optical property contrasts throughout the Atlantic Ocean revealed using flow cytometryApplied Optics, doi: 10.1364/AO.58.008802

Andrea Storto, Aida Alvera-Azcárate, Magdalena A. Balmaseda, Alexander Barth, Matthieu Chevallier, Francois Counillon, Catia M. Domingues, Marie Drevillon, Yann Drillet, Gaël Forget, Gilles Garric, Keith Haines, Fabrice Hernandez, Doroteaciro Iovino, Laura C. Jackson, Jean-Michel Lellouche, Simona Masina, Michael Mayer, Peter R. Oke, Stephen G. Penny, K. Andrew Peterson, Chunxue Yang and Hao Zuo (2019), Ocean Reanalyses: Recent Advances and Unsolved ChallengesFrontiers of Marine Science, doi: 10.3389/fmars.2019.00418

David Talmy, Stephen J. Beckett, Darcy A.A. Taniguchi, Corina P.D. Brussard, Joshua S. Weitz, and Michael J. Follows (2019), An empirical model of carbon flow through marine viruses and microzooplankton grazers, Environmental Microbiology, doi: 10.1111/1462-2920.14626

Wagner, C.C, H.M. Amos, C.P. Thackray, Y. Zhang, E.W. Lundgren, G. Forget, C.L. Friedman, N.E. Selin, R. Lohmann, E.M. Sunderland (2019), A global 3‐D ocean model for polychlorinated biphenyls (PCBs): Benchmark compounds for understanding the impacts of global change on neutral persistent organic pollutants, Global Biogeochemical Cycles, doi: 10.1029/2018GB006018

Emily J. Zakem, Amala Mahadevan, Jonathan M. Lauderdale, and Michael J. Follows (2019), Stable aerobic and anaerobic coexistence in anoxic marine zones, The ISME Journal, doi: 10.1038/s41396-019-0523-8

2018

Ajani, P.A., N. McGinty, Z.V. Finkel, and A.J. Irwin (2018), Phytoplankton realized niches track changing oceanic conditions at a long-term coastal station off Sydney AustraliaFrontiers in Marine Science, 5: 285, doi: 10.3389/fmars.2018.00285

Amrhein, D.E., C. Wunsch, O. Marchal, G. Forget (2018), A global glacial ocean state estimate constrained by upper-ocean temperature proxies, Journal of Climate, doi: 10.1175/JCLI-D-17-0769.1

Bouman, H.A., T. Platt, M. Doblin, M., M.G. Figueiras, K. Gudmundsson, H.G. Gudfinnsson, B. Huang, A. Hickman, M. Hiscock, T. Jackson, V.A. Lutz, F. Mélin, F. Rey, P. Pepin, V. Segura, G.H. Tilstone, V. van Dongen-Vogels, S. Sathyendranath (2018), Photosynthesis–irradiance parameters of marine phytoplankton: synthesis of a global data setEarth System Science Data, doi: 10.5194/essd-10-251-2018

Cael, B.B., M.C.G. Carlson, C.L. Follett, and M.J. Follows (2018), Marine virus-like particles and microbes: a linear interpretation, Frontiers in Microbiology, doi: 10.3389/fmicb.2018.00358

Cael, B.B., K. Bisson, and C. L. Follett (2018), Can ocean primary production and biological carbon export be related through their probability distributions? Global Biogeochemical Cycles, doi: 10.1029/2017GB005797

Follett, C.L., A.E. White, S.T. Wilson, M.J. Follows (2018), Nitrogen Fixation Rates Diagnosed from Diurnal Changes in Elemental Stoichiometry, Limnology and Oceanography dot: 10.1002/lno.10815

Inomura, K., J. Bragg, L. Riemann, and M.J. Follows (2018), A mechanistic model of nitrogen fixation in the presence of ammoniumPLoS One, doi: 10.1371/journal.pone.0208282

Jones, D.C., G. Forget, B. Sinha, S.A. Josey, E.J.D. Boland, A.J.S Meijers and E. Shuckburgh (2018), Local and remote influences on the heat content of the Labrador Sea: An adjoint sensitivity study, Journal of Geophysical Research: Oceans, 123, 2646‐2667, doi: 10.1002/2018JC013774

Kovac, Ž., T. Platt, S. Sathyendranath and S. Lomas (2018), Extraction of photosynthesis parameters from time series measurements of in situ production: Bermuda Atlantic Time-Series Study Remote Sensing, Remote Sensing, doi: 10.3390/rs10060915

Mattern, J.P. and C.A. Edwards (2018), A simple difference quotient-based approximation for biogeochemical tangent linear and adjoint modelsJournal of Geophysical Research – Oceans, doi: 10.1029/2018JC014283

McGinty, N., A.D. Barton, N.R. Record, Z.V. Finkel, A.J. Irwin (2018), Traits structure copepod niches in the North Atlantic and Southern Ocean, Marine Ecology Progress Series, doi: 10.3354/meps12660

Strobach, E., A. Molod, G. Forget, J-M. Campin, C. Hill, D. Menemenlis, P. Heimbach (2018), Consequences of different air-sea feedbacks on ocean using MITgcm and MERRA-2 forcing: Implications for Coupled Data Assimilation Systems, Ocean Modelling, doi: 10.1016/j.ocemod.2018.10.006

Vallino, J.J. and J.A. Huber (2018),  Using maximum entropy production to describe microbial biogeochemistry over time and space in a meromictic pond, Frontiers in Environmental Science, doi: 10.3389/fenvs.2018.00100

2017

Jackson, T, S. Sathyendranath, T. Platt (2017), An exact solution for modelling photoacclimation of the carbon-to-chlorophyll ratio in Phytoplankton, Frontiers in Marine Science, doi: 10.3389/fmars.2017.00283

Platt, T, S. Sathyendranath, G.N. White III, T. Jackson, S. Saux-Picart, H. Bouman (2017), Phytoplankton production as archived data: sensitivity to surface irradianceFrontiers in Marine Science, doi: 10.3389/fmars.2017.00387

CBIOMES members in bold.


 

CBIOMES members: per Simons Foundation policy publications resulting from projects supported by the Simons Foundation are required to carry a specifically worded acknowledgment.

For CBIOMES that language is:

“This work was supported by the Simons Collaboration on Computational Biogeochemical Modeling of Marine Ecosystems/CBIOMES) (Grant Id: XXXXX, Awardee Initials).”

CBIOMES grant numbers are listed here [restricted]