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Shengwei Hou, Siliangyu Cheng, Ting Chen, Jed A. Fuhrman (2021), DeepMicrobeFinder Sorts Metagenomes into Prokaryotes, Eukaryotes and Viruses, with Marine Applications, Microbiome (in review), doi: 10.21203/

Sangwon Hyun, Aditya Mishra, Christopher L. Follett, Bror Jonsson, Gemma Kulk, Gael Forget, Marie-Fanny Racault, Thomas Jackson. Stephanie Dutkiewicz, Christion L. Mueller, Jacob Bien (2021), Ocean Mover’s Distance: Using Optimal Transport for Analyzing Oceanographic Data, arXiv: 2111.08736 [stat.AP] (accepted for publication in Proceedings of the Royal Society A.)

Sangwon Hyun, Mattias Rolf Cape, Francois Ribalet, and Jacob Bien (2021), Modeling Cell Populations Measured By Flow Cytometry With Covariates Using Sparse Mixture of Regressions, arXiv:2008.11521 [stat.AP]

Ignacio-Espinoza, J. Cesar, Sarah M. Laperriere, Yi-Chun Yeh, Jake Weissman, Shengwei Hou, Andrew M. Long, & Jed A. Fuhrman (2021), Ribosome-linked mRNA-rRNA chimeras reveal active novel virus-host associations, bioRxiv (submitted to Nature Microbiology)

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 (in press)

Dalit Roth-Rosenberg, Dikla Aharonovich, Anne-Willem Omta, Michael J. Follows, Daniel Sher (2021), Dynamic macromolecular composition and high exudation rates in Prochlorococcus, bioRXiv:10.1101/828897

Ioannis Tsakalakis, Michael J. Follows, Stephanie Dutkiewicz, Christopher L. Follett, Joseph J. Vallino (2021), Diel light cycles affect phytoplankton competition in the global ocean, bioRxiv (submitted to Global Ecology and Biogeography)

Other Submitted, and in Preparation Manuscripts

In-process papers are now listed here




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

Vinitha Ebenezer, Yingyu 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

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

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

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

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

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


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

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. 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

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, Yingyu 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


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


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 @

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


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


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

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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).”

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