tmp

@article{Caron2016,
abstract = {Protists, which are single-celled eukaryotes, critically influence the ecology and chemistry of marine ecosystems, but genome-based studies of these organisms have lagged behind those of other microorganisms. However, recent transcriptomic studies of cultured species, complemented by meta-omics analyses of natural communities, have increased the amount of genetic information available for poorly represented branches on the tree of eukaryotic life. This information is providing insights into the adaptations and interactions between protists and other microorganisms and macroorganisms, but many of the genes sequenced show no similarity to sequences currently available in public databases. A better understanding of these newly discovered genes will lead to a deeper appreciation of the functional diversity and metabolic processes in the ocean. In this Review, we summarize recent developments in our understanding of the ecology, physiology and evolution of protists, derived from transcriptomic studies of cultured strains and natural communities, and discuss how these novel large-scale genetic datasets will be used in the future.},
author = {Caron, David A. and Alexander, Harriet and Allen, Andrew E. and Archibald, John M. and Armbrust, E. Virginia and Bachy, Charles and Bell, Callum J. and Bharti, Arvind and Dyhrman, Sonya T. and Guida, Stephanie M. and Heidelberg, Karla B. and Kaye, Jonathan Z. and Metzner, Julia and Smith, Sarah R. and Worden, Alexandra Z.},
doi = {10.1038/nrmicro.2016.160},

journal = {Nature Reviews Microbiology},
mendeley-groups = {Oped{\_}Reanalysis},
month = {nov},
number = {1},
pages = {6--20},
publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
title = {{Probing the evolution, ecology and physiology of marine protists using transcriptomics}},

volume = {15},
year = {2016}
}

@article{Rouco2016,
author = {Rouco, M{\'{o}}nica and Haley, Sheean T. and Alexander, Harriet and Wilson, Samuel T. and Karl, David M. and Dyhrman, Sonya T.},
doi = {10.1111/1758-2229.12488},
file = {:Users/halexand/Library/Application Support/Mendeley Desktop/Downloaded/Rouco et al. - 2016 - Variable depth distribution of iTrichodesmiumi clades in the North Pacific Ocean.pdf:pdf},

journal = {Environmental Microbiology Reports},
month = {oct},
title = {{Variable depth distribution of \textit{Trichodesmium} clades in the North Pacific Ocean}},

year = {2016}
}


@article{Alexander2015a,
author = {Alexander, Harriet and Rouco, M{\'{o}}nica and Haley, Sheean T. and Wilson, Samuel T. and Karl, David M. and Dyhrman, Sonya T.},
doi = {10.1073/pnas.1518165112},

journal = {Proceedings of the National Academy of Sciences},
month = {nov},
number = {44},
pages = {E5972--E5979},
title = {{Functional group-specific traits drive phytoplankton dynamics in the oligotrophic ocean}},

volume = {112},
year = {2015}
}

@article{Alexander2015,
author = {Alexander, Harriet and Jenkins, Bethany D. and Rynearson, Tatiana A. and Dyhrman, Sonya T.},
doi = {10.1073/pnas.1421993112},

journal = {Proceedings of the National Academy of Sciences},
month = {apr},
number = {17},
pages = {E2182--E2190},
title = {{Metatranscriptome analyses indicate resource partitioning between diatoms in the field}},

volume = {112},
year = {2015}
}
@article{Fischer2014,
author = {Fischer, Alexis and Moberg, Emily and Alexander, Harriet and Brownlee, Emily and Hunter-Cevera, Kristen and Pitz, Kathleen and Rosengard, Sarah and Sosik, Heidi},
doi = {10.5670/oceanog.2014.26},

journal = {Oceanography},
month = {mar},
number = {1},
pages = {222--235},
title = {{Sixty Years of Sverdrup: A Retrospective of Progress in the Study of Phytoplankton Blooms}},

volume = {27},
year = {2014}
}
@article{Alexander2012,
author = {Alexander, Harriet and Jenkins, Bethany D and Rynearson, Tatiana A and Saito, Mak A and Mercier, Melissa L and Dyhrman, Sonya T},
doi = {10.3389/fmicb.2012.00385},
file = {:Users/harrietalexander/Library/Application Support/Mendeley Desktop/Downloaded/Alexander et al. - 2012 - Identifying reference genes with stable expression from high throughput sequence data(2).pdf:pdf},


journal = {Frontiers in Microbiology},
keywords = {Diatoms,diatom,h,housekeeping genes,phytoplankton,reference gene,relative gene expression,rt-qpcr,thalassiosira pseudonana,transcriptome},
language = {English},
month = {jan},
number = {November},
pages = {385},
pmid = {23162540},
publisher = {Frontiers},
title = {{Identifying reference genes with stable expression from high throughput sequence data}},

volume = {3},
year = {2012}
}
@article{Dyhrman2012,
author = {Dyhrman, Sonya T and Jenkins, Bethany D and Rynearson, Tatiana A and Saito, Mak A and Mercier, Melissa L and Alexander, Harriet and Whitney, Leann P and Drzewianowski, Andrea and Bulygin, Vladimir V and Bertrand, Erin M and Wu, Zhijin and Benitez-Nelson, Claudia and Heithoff, Abigail},
doi = {10.1371/journal.pone.0033768},
file = {:Users/harrietalexander/Library/Application Support/Mendeley Desktop/Downloaded/Dyhrman et al. - 2012 - The transcriptome and proteome of the diatom Thalassiosira pseudonana reveal a diverse phosphorus stress response.pdf:pdf},

journal = {PloS one},
keywords = {Biological Transport,Diatoms,Diatoms: genetics,Diatoms: metabolism,Glycolysis,Glycolysis: genetics,Phosphorus,Phosphorus: metabolism,Physiological,Protein Biosynthesis,Protein Biosynthesis: genetics,Proteome,Stress,Transcriptome,proteome,transcriptome},
mendeley-tags = {proteome,transcriptome},
month = {jan},
number = {3},
pages = {e33768},
pmid = {22479440},
title = {{The transcriptome and proteome of the diatom \textit{Thalassiosira pseudonana} reveal a diverse phosphorus stress response.}},

volume = {7},
year = {2012}
}
@article{Rouco2018,
author = {Rouco, M{\'{o}}nica and Frischkorn, Kyle R. and Haley, Sheean T. and Alexander, Harriet and Dyhrman, Sonya T.},
doi = {10.1038/s41396-018-0087-z},

journal = {The ISME Journal},
month = {jun},
number = {6},
pages = {1486--1495},
title = {{Transcriptional patterns identify resource controls on the diazotroph \textit{Trichodesmium} in the Atlantic and Pacific oceans}},

volume = {12},
year = {2018}
}
@article{Hu2018,
author = {Hu, Sarah K and Liu, Zhenfeng and Alexander, Harriet and Campbell, Victoria and Connell, Paige E and Dyhrman, Sonya T and Heidelberg, Karla B and Caron, David A},
doi = {10.1111/1462-2920.14259},

journal = {Environmental Microbiology},
month = {apr},
title = {{Shifting metabolic priorities among key protistan taxa within and below the euphotic zone}},

year = {2018}
}
@article{Kujawinski2017,
author = {Kujawinski, Elizabeth B and Longnecker, Krista and Alexander, Harriet and Dyhrman, Sonya T and Fiore, Cara L and Haley, Sheean T and Johnson, Winifred M},
journal = {Limnology and Oceanography Letters},
number = {4},
pages = {119--129},
title = {{Phosphorus availability regulates intracellular nucleotides in marine eukaryotic phytoplankton}},
volume = {2},
year = {2017}
}
@article{Guy-Haim2017,
author = {Guy-Haim, Tamar and Alexander, Harriet and Bell, Tom W. and Bier, Raven L. and Bortolotti, Lauren E. and Brise{\~{n}}o-Avena, Christian and Dong, Xiaoli and Flanagan, Alison M. and Grosse, Julia and Grossmann, Lars and Hasnain, Sarah and Hovel, Rachel and Johnston, Cora A. and Miller, Dan R. and Muscarella, Mario and Noto, Akana E. and Reisinger, Alexander J. and Smith, Heidi J. and Stamieszkin, Karen},
doi = {10.1186/s13750-017-0084-0},

journal = {Environmental Evidence},
month = {dec},
number = {1},
pages = {6},
title = {{What are the type, direction, and strength of species, community, and ecosystem responses to warming in aquatic mesocosm studies and their dependency on experimental characteristics? A systematic review protocol}},

volume = {6},
year = {2017}
}
@article{Durden2017,
abstract = {{\textcopyright} 2017 Association for the Sciences of Limnology and Oceanography. Got “Big Data“? Not sure how best to use it? Big Data is becoming an important facet of aquatic ecology, and researchers must learn to harness it to reap the rewards of using it. The benefits of using Big Data are many, and include advancements in scientific understanding at larger scales and higher resolution, applications to improving environmental management and policy, and public engagement. We aim to demystify the use of Big Data for individual scientists, and provide some food for thought for the aquatic ecology community on how to develop this sphere. To achieve this, we highlight six key challenges: (1) how to recognize if you have Big Data, (2) handling Big Data, (3) issues with classical analytical techniques, (4) verification of Big Data, (5) considerations for data sharing, and (6) community development of knowledge infrastructures. We then present approaches and tools which have been successfully applied to these challenges in aquatic ecology and other scientific fields.},
author = {Durden, J.M. and Luo, J.Y. and Alexander, H. and Flanagan, A.M. and Grossmann, L.},
doi = {10.1002/lob.10213},

journal = {Limnology and Oceanography Bulletin},
title = {{Integrating ''big data`` into aquatic ecology: Challenges and opportunities}},
year = {2017}
}
@article{Haley2017,
abstract = {{\textcopyright} 2017 Elsevier B.V. The marine eukaryotic alga Heterosigma akashiwo (Raphidophyceae) is known for forming ichthyotoxic harmful algal blooms (HABs). In the past 50 years, H. akashiwo blooms have increased, occurring globally in highly eutrophic coastal and estuarine systems. These systems often incur dramatic physicochemical changes, including macronutrient (nitrogen and phosphorus) enrichment and depletion, on short timescales. Here, H. akashiwo cultures grown under nutrient replete, low N and low P growth conditions were examined for changes in biochemical and physiological characteristics in concert with transcriptome sequencing to provide a mechanistic perspective on the metabolic processes involved in responding to N and P stress. There was a marked difference in the overall transcriptional pattern between low N and low P transcriptomes. Both nutrient stresses led to significant changes in the abundance of thousands of contigs related to a wide diversity of metabolic pathways, with limited overlap between the transcriptomic responses to low N and low P. Enriched contigs under low N included many related to nitrogen metabolism, acquisition, and transport. In addition, metabolic modules like photosynthesis and carbohydrate metabolism changed significantly under low N, coincident with treatment-specific changes in photosynthetic efficiency and particulate carbohydrate content. P-specific contigs responsible for P transport and organic P use were more enriched in the low P treatment than in the replete control and low N treatment. These results provide new insight into the genetic mechanisms that distinguish how this HAB species responds to these two common nutrient stresses, and the results can inform future field studies, linking transcriptional patterns to the physiological ecology of H. akashiwo in situ.},
author = {Haley, Sheean T. and Alexander, Harriet and Juhl, Andrew R. and Dyhrman, Sonya T.},
doi = {10.1016/j.hal.2017.07.001},

journal = {Harmful Algae},
keywords = {De novo assembly,Gene expression,Harmful algal bloom,Heterosigma akashiwo,Phytoplankton,Transcriptome},
month = {sep},
pages = {258--270},
title = {{Transcriptional response of the harmful raphidophyte \textit{Heterosigma akashiwo} to nitrate and phosphate stress}},

volume = {68},
year = {2017}
}
@article{Harke2017,
author = {Harke, Matthew J. and Juhl, Andrew R. and Haley, Sheean T. and Alexander, Harriet and Dyhrman, Sonya T.},
doi = {10.3389/fmicb.2017.01279},

journal = {Frontiers in Microbiology},
keywords = {Conserved response,MMETSP,Nitrogen,Phosphorus,Phytoplankton,Transcriptome},
month = {jul},
number = {JUL},
title = {{Conserved transcriptional responses to nutrient stress in bloom-forming algae}},

volume = {8},
year = {2017}
}
@article{Moniruzzaman2017,
author = {Moniruzzaman, Mohammad and Wurch, Louie L. and Alexander, Harriet and Dyhrman, Sonya T. and Gobler, Christopher J. and Wilhelm, Steven W.},
doi = {10.1038/ncomms16054},

journal = {Nature Communications},
month = {jun},
pages = {16054},
title = {{Virus-host relationships of marine single-celled eukaryotes resolved from metatranscriptomics}},

volume = {8},
year = {2017}
}