219
Hook SE, Osborn HL (2012) Comparison of toxicity and transcriptomic profiles in a diatom exposed to oil, dispersants, dispersed oil. Aquat Toxicol Amst Neth 124–125:139–151.
doi:10.1016/j.aquatox.2012.08.005
Ideker T, Galitski T, Hood L (2001) A NEW APPROACH TO DECODING LIFE: systems biology.
Annu Rev Genomics Hum Genet 2:343–372. doi:10.1146/annurev.genom.2.1.343
Iverson V, Morris RM, Frazar CD et al (2012) Untangling genomes from Metagenomes: revealing an uncultured class of marine Euryarchaeota. Science 335:587–590. doi:10.1126/
science.1212665
Karr JR, Sanghvi JC, Macklin DN et al (2012) A whole-cell computational model predicts phenotype from genotype. Cell 150:389–401. doi:10.1016/j.cell.2012.05.044
Karsenti E, Acinas SG, Bork P et al (2011) A holistic Approach to marine eco-systems biology.
PLoS Biol 9:e1001177. doi:10.1371/journal.pbio.1001177
Keeling PJ, Burki F, Wilcox HM et al (2014) The marine microbial eukaryote Transcriptome
sequencing project (MMETSP): illuminating the functional diversity of eukaryotic life in
the oceans through transcriptome sequencing. PLoS Biol 12:e1001889. doi:10.1371/journal.
pbio.1001889
Kim J, Fabris M, Baart G et al (2016) Flux balance analysis of primary metabolism in the diatom
Phaeodactylum tricornutum. Plant J 85:161–176. doi:10.1111/tpj.13081
Kusebauch U, Campbell DS, Deutsch EW et al (2016) Human SRMAtlas: a resource of targeted assays to quantify the complete human proteome. Cell 166:766–778. doi:10.1016/j.
cell.2016.06.041
Levering J, Broddrick J, Dupont CL et al (2016) Genome-scale model reveals metabolic basis
of biomass partitioning in a model diatom. PLoS One 11:e0155038. doi:10.1371/journal.
pone.0155038
Levering J, Dupont CL, Allen AE, et al (2017) Integrated regulatory and metabolic networks of the
marine diatom Phaeodactylum tricornutum predict the response to rising CO2 levels. mSystems 2:e00142-16. doi: 10.1128/mSystems.00142-16
Lin S, Cheng S, Song B, Zhong X, Lin X, Li W, Li L, Zhang Y, Zhang H, Ji Z, Cai M, Zhuang Y,
Shi X, Lin L, Wang L, Wang Z, Liu X, Yu S, Zeng P, Hao H, Zou Q, Chen C, Li Y, Wang Y, Xu
C, Meng S, Xu X, Wang J, Yang H, Campbell DA, Sturm NR, Dagenais-Bellefeuille S, Morse
D (2015) The Symbiodinium kawagutii genome illuminates dinoflagellate gene expression and
coral symbiosis. Science 350(6261):691–694
Lommer M, Specht M, Roy A-S, Kraemer L, Andreson R, Gutowska MA, Wolf J, Bergner SV,
Schilhabel MB, Klostermeier UC, Beiko RG, Rosenstiel P, Hippler M, LaRoche J (2012)
Genome and low-iron response of an oceanic diatom adapted to chronic iron limitation.
Genome Biol 13(7):R66
Marchetti A, Schruth DM, Durkin CA et al (2012) Comparative metatranscriptomics identifies
molecular bases for the physiological responses of phytoplankton to varying iron availability.
PNAS 2012 109 (6) E317–E325. doi:10.1073/pnas.1118408109
Marchetti A, Moreno CM, Cohen NR, Oleinikov I, deLong K, Twining BS, Armbrust VE, Lampe
RH, Müller K (2017) Development of a molecular-based index for assessing iron status in
bloom-forming pennate diatoms. J Phycol 53(4):820–832
Merchant SS, Prochnik SE, Vallon O et al (2007) The Chlamydomonas genome reveals the evolution of key animal and Plant functions. Science 318:245–250. doi:10.1126/science.1143609
Mock T, Samanta MP, Iverson V et al (2008) Whole-genome expression profiling of the marine
diatom Thalassiosira pseudonana identifies genes involved in silicon bioprocesses. Proc Natl
Acad Sci U S A 105:1579–1584. doi:10.1073/pnas.0707946105
Mock T, Otillar RP, Strauss J, McMullan M, Paajanen P, Schmutz J, Salamov A, Sanges R,
Toseland A, Ward BJ, Allen AE, Dupont CL, Frickenhaus S, Maumus F, Veluchamy A, Wu T,
Barry KW, Falciatore A, Ferrante MI, Fortunato AE, Glöckner G, Gruber A, Hipkin R, Janech
MG, Kroth PG, Leese F, Lindquist EA, Lyon BR, Martin J, Mayer C, Parker M, Quesneville H,
Raymond JA, Uhlig C, Valas RE, Valentin KU, Worden AZ, Virginia Armbrust E, Clark MD,
10 Marine Microalgae: Systems Biology from ‘Omics’
Hook SE, Osborn HL (2012) Comparison of toxicity and transcriptomic profiles in a diatom exposed to oil, dispersants, dispersed oil. Aquat Toxicol Amst Neth 124–125:139–151.
doi:10.1016/j.aquatox.2012.08.005
Ideker T, Galitski T, Hood L (2001) A NEW APPROACH TO DECODING LIFE: systems biology.
Annu Rev Genomics Hum Genet 2:343–372. doi:10.1146/annurev.genom.2.1.343
Iverson V, Morris RM, Frazar CD et al (2012) Untangling genomes from Metagenomes: revealing an uncultured class of marine Euryarchaeota. Science 335:587–590. doi:10.1126/
science.1212665
Karr JR, Sanghvi JC, Macklin DN et al (2012) A whole-cell computational model predicts phenotype from genotype. Cell 150:389–401. doi:10.1016/j.cell.2012.05.044
Karsenti E, Acinas SG, Bork P et al (2011) A holistic Approach to marine eco-systems biology.
PLoS Biol 9:e1001177. doi:10.1371/journal.pbio.1001177
Keeling PJ, Burki F, Wilcox HM et al (2014) The marine microbial eukaryote Transcriptome
sequencing project (MMETSP): illuminating the functional diversity of eukaryotic life in
the oceans through transcriptome sequencing. PLoS Biol 12:e1001889. doi:10.1371/journal.
pbio.1001889
Kim J, Fabris M, Baart G et al (2016) Flux balance analysis of primary metabolism in the diatom
Phaeodactylum tricornutum. Plant J 85:161–176. doi:10.1111/tpj.13081
Kusebauch U, Campbell DS, Deutsch EW et al (2016) Human SRMAtlas: a resource of targeted assays to quantify the complete human proteome. Cell 166:766–778. doi:10.1016/j.
cell.2016.06.041
Levering J, Broddrick J, Dupont CL et al (2016) Genome-scale model reveals metabolic basis
of biomass partitioning in a model diatom. PLoS One 11:e0155038. doi:10.1371/journal.
pone.0155038
Levering J, Dupont CL, Allen AE, et al (2017) Integrated regulatory and metabolic networks of the
marine diatom Phaeodactylum tricornutum predict the response to rising CO2 levels. mSystems 2:e00142-16. doi: 10.1128/mSystems.00142-16
Lin S, Cheng S, Song B, Zhong X, Lin X, Li W, Li L, Zhang Y, Zhang H, Ji Z, Cai M, Zhuang Y,
Shi X, Lin L, Wang L, Wang Z, Liu X, Yu S, Zeng P, Hao H, Zou Q, Chen C, Li Y, Wang Y, Xu
C, Meng S, Xu X, Wang J, Yang H, Campbell DA, Sturm NR, Dagenais-Bellefeuille S, Morse
D (2015) The Symbiodinium kawagutii genome illuminates dinoflagellate gene expression and
coral symbiosis. Science 350(6261):691–694
Lommer M, Specht M, Roy A-S, Kraemer L, Andreson R, Gutowska MA, Wolf J, Bergner SV,
Schilhabel MB, Klostermeier UC, Beiko RG, Rosenstiel P, Hippler M, LaRoche J (2012)
Genome and low-iron response of an oceanic diatom adapted to chronic iron limitation.
Genome Biol 13(7):R66
Marchetti A, Schruth DM, Durkin CA et al (2012) Comparative metatranscriptomics identifies
molecular bases for the physiological responses of phytoplankton to varying iron availability.
PNAS 2012 109 (6) E317–E325. doi:10.1073/pnas.1118408109
Marchetti A, Moreno CM, Cohen NR, Oleinikov I, deLong K, Twining BS, Armbrust VE, Lampe
RH, Müller K (2017) Development of a molecular-based index for assessing iron status in
bloom-forming pennate diatoms. J Phycol 53(4):820–832
Merchant SS, Prochnik SE, Vallon O et al (2007) The Chlamydomonas genome reveals the evolution of key animal and Plant functions. Science 318:245–250. doi:10.1126/science.1143609
Mock T, Samanta MP, Iverson V et al (2008) Whole-genome expression profiling of the marine
diatom Thalassiosira pseudonana identifies genes involved in silicon bioprocesses. Proc Natl
Acad Sci U S A 105:1579–1584. doi:10.1073/pnas.0707946105
Mock T, Otillar RP, Strauss J, McMullan M, Paajanen P, Schmutz J, Salamov A, Sanges R,
Toseland A, Ward BJ, Allen AE, Dupont CL, Frickenhaus S, Maumus F, Veluchamy A, Wu T,
Barry KW, Falciatore A, Ferrante MI, Fortunato AE, Glöckner G, Gruber A, Hipkin R, Janech
MG, Kroth PG, Leese F, Lindquist EA, Lyon BR, Martin J, Mayer C, Parker M, Quesneville H,
Raymond JA, Uhlig C, Valas RE, Valentin KU, Worden AZ, Virginia Armbrust E, Clark MD,
10 Marine Microalgae: Systems Biology from ‘Omics’