Algal omics: unlocking bioproduct diversity in algae cell factories

Microalgal triacylglycerols as feedstocks for biofuel production: perspectives and advances

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The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions

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Applications of next-generation sequencing technologies in functional genomics

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Genetic Engineering of Algae for Enhanced Biofuel Production

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Chloroplast Transformation in Chlamydomonas with High Velocity Microprojectiles

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Carotenoids in Algae: Distributions, Biosyntheses and Functions

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Protein function in the post-genomic era

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Microalgal biofactories: A promising approach towards sustainable omega-3 fatty acid production

Adarme-Vega, T. C., Lim, D. K. Y., Timmins, M., Vernen, F., Li, Y., & Schenk, P. M. (2012) · Microbial Cell Factories · doi:10.1186/1475-2859-11-96 · Cited by 641 · see citing works

FERMENTATIVE AND PHOTOCHEMICAL PRODUCTION OF HYDROGEN IN ALGAE

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A green light for engineered algae: redirecting metabolism to fuel a biotechnology revolution

Rosenberg, J. N., Oyler, G. A., Wilkinson, L., & Betenbaugh, M. J. (2008) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2008.07.008 · Cited by 631 · see citing works

Changes in Transcript Abundance in <i>Chlamydomonas reinhardtii</i> following Nitrogen Deprivation Predict Diversion of Metabolism

Miller, R., Wu, G., Deshpande, R. R., Vieler, A., Gärtner, K., Li, X., Moellering, E. R., Zäuner, S., Cornish, A. J., Liu, B., et al. (2010) · PLANT PHYSIOLOGY · doi:10.1104/pp.110.165159 · Cited by 511 · see citing works

Three Acyltransferases and Nitrogen-responsive Regulator Are Implicated in Nitrogen Starvation-induced Triacylglycerol Accumulation in Chlamydomonas

Boyle, N. R., Page, M. D., Liu, B., Blaby, I. K., Casero, D., Kropat, J., Cokus, S. J., Hong‐Hermesdorf, A., Shaw, J., Karpowicz, S. J., et al. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.334052 · Cited by 416 · see citing works

RNA Interference Silencing of a Major Lipid Droplet Protein Affects Lipid Droplet Size in Chlamydomonas reinhardtii

Moellering, E. R., & Christoph Benning, A. (2009) · Eukaryotic Cell · doi:10.1128/ec.00203-09 · Cited by 401 · see citing works

Algae biofuels: versatility for the future of bioenergy

Jones, C. S., & Mayfield, S. P. (2011) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2011.10.013 · Cited by 400 · see citing works

COMMERCIAL DEVELOPMENTS IN MICROALGAL BIOTECHNOLOGY

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Metabolic and gene expression changes triggered by nitrogen deprivation in the photoautotrophically grown microalgae Chlamydomonas reinhardtii and Coccomyxa sp. C-169

Msanne, J., Xu, D., Konda, A. R., Casas-Mollano, J. A., Awada, T. N., Cahoon, E. B., & Cerutti, H. D. (2012) · Phytochemistry · doi:10.1016/j.phytochem.2011.12.007 · Cited by 389 · see citing works

Hydrogenases and Hydrogen Photoproduction in Oxygenic Photosynthetic Organisms

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A chloroplast pathway for the de novo biosynthesis of triacylglycerol in<i>Chlamydomonas reinhardtii</i>

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Expression and assembly of a fully active antibody in algae

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Transgenic microalgae as green cell-factories

León, R. (2003) · Trends in biotechnology · doi:10.1016/j.tibtech.2003.11.003 · Cited by 328 · see citing works

Anaerobic Acclimation in Chlamydomonas reinhardtii

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Micro-algae come of age as a platform for recombinant protein production

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A Comparison of Labeling and Label-Free Mass Spectrometry-Based Proteomics Approaches

Patel, V. J., Thalassinos, K., Slade, S. E., Connolly, J. B., Crombie, A. T., Murrell, J. C., & Scrivens, J. H. (2009) · Journal of Proteome Research · doi:10.1021/pr900080y · Cited by 259 · see citing works

Isoprenoid biosynthesis in eukaryotic phototrophs: A spotlight on algae

Lohr, M., Schwender, J., & Polle, J. E. W. (2011) · Plant Science · doi:10.1016/j.plantsci.2011.07.018 · Cited by 244 · see citing works

Robust Expression and Secretion of Xylanase1 in Chlamydomonas reinhardtii by Fusion to a Selection Gene and Processing with the FMDV 2A Peptide

Rasala, B. A., Lee, P. A., Shen, Z., Briggs, S. P., Mendez, M. J., & Mayfield, S. P. (2012) · PLoS ONE · doi:10.1371/journal.pone.0043349 · Cited by 234 · see citing works

Transcriptomics: Advances and approaches

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Examination of Triacylglycerol Biosynthetic Pathways via De Novo Transcriptomic and Proteomic Analyses in an Unsequenced Microalga

Guarnieri, M. T., Nag, A., Smolinski, S. L., Darzins, A., Seibert, M., & Pienkos, P. T. (2011) · PLoS ONE · doi:10.1371/journal.pone.0025851 · Cited by 234 · see citing works

Proteomic profiling of oil bodies isolated from the unicellular green microalga Chlamydomonas reinhardtii: With focus on proteins involved in lipid metabolism

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Transcriptomic analysis of the oleaginous microalga Neochloris oleoabundans reveals metabolic insights into triacylglyceride accumulation

Rismani‐Yazdi, H., HAZNEDAROĞLU, B. Z., Hsin, C., & Peccia, J. (2012) · Biotechnology for Biofuels · doi:10.1186/1754-6834-5-74 · Cited by 213 · see citing works

Enhancement of carotenoids biosynthesis in Chlamydomonas reinhardtii by nuclear transformation using a phytoene synthase gene isolated from Chlorella zofingiensis

Cordero, B. F., Couso, I., León, R., Rodrı́guez, H., & Vargas, M. A. (2011) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-011-3262-y · Cited by 190 · see citing works

Production of unique immunotoxin cancer therapeutics in algal chloroplasts

Tran, M., Van, C., Barrera, D. J., Pettersson, P. L., Peinado, C. D., Bui, J. D., & Mayfield, S. P. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1214638110 · Cited by 186 · see citing works

Genome-Based Examination of Chlorophyll and Carotenoid Biosynthesis in Chlamydomonas reinhardtii

Lohr, M., Im, C.-S., & Grossman, A. R. (2005) · PLANT PHYSIOLOGY · doi:10.1104/pp.104.056069 · Cited by 169 · see citing works

Influence of nitrogen-limitation regime on the production byChlorella vulgarisof lipids for biodiesel feedstocks

Stephenson, A. L., Dennis, J. S., Howe, C. J., Scott, S. A., & Smith, A. G. (2010) · Biofuels · doi:10.4155/bfs.09.1 · Cited by 162 · see citing works

Identification of unique mechanisms for triterpene biosynthesis in Botryococcus braunii

Niehaus, T. D., Okada, S., Devarenne, T. P., Watt, D. S., Sviripa, V. M., & Chappell, J. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1106222108 · Cited by 159 · see citing works

Novel metabolism in Chlamydomonas through the lens of genomics

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Development of Synechocystis sp. PCC 6803 as a Phototrophic Cell Factory

Yu, Y., You, L., Liu, D., Hollinshead, W. D., Tang, Y., & Zhang, F. (2013) · Marine Drugs · doi:10.3390/md11082894 · Cited by 154 · see citing works

Recent advances of metabolomics in plant biotechnology

Okazaki, Y., & Saito, K. (2011) · Plant Biotechnology Reports · doi:10.1007/s11816-011-0191-2 · Cited by 151 · see citing works

Cadmium response and redoxin targets in Chlamydomonas reinhardtii: a proteomic approach

Gillet, S., Decottignies, P., Chardonnet, S., & Maréchal, P. L. (2006) · Photosynthesis Research · doi:10.1007/s11120-006-9108-2 · Cited by 149 · see citing works

Transcriptome for Photobiological Hydrogen Production Induced by Sulfur Deprivation in the Green Alga Chlamydomonas reinhardtii

Nguyen, A. V., Thomas‐Hall, S. R., Malnoë, A., Timmins, M., Mussgnug, J. H., Rupprecht, J., Kruse, O., Hankamer, B. D., & Schenk, P. M. (2008) · Eukaryotic Cell · doi:10.1128/ec.00418-07 · Cited by 141 · see citing works

Whole transcriptome analysis of the silicon response of the diatom Thalassiosira pseudonana

Shrestha, R. P., Tesson, B., Norden‐Krichmar, T. M., et al. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-499 · Cited by 138 · see citing works

Alga-Produced Cholera Toxin-Pfs25 Fusion Proteins as Oral Vaccines

Gregory, J. A., Topol, A. B., Doerner, D. Z., & Mayfield, S. P. (2013) · Applied and Environmental Microbiology · doi:10.1128/aem.00714-13 · Cited by 132 · see citing works

Stable nuclear transformation of Chlamydomonas reinhardtii by using a C. reinhardtii gene as the selectable marker.

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Biological Conversion of Light Energy to the Chemical Energy of Methane

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The GreenCut2 Resource, a Phylogenomically Derived Inventory of Proteins Specific to the Plant Lineage

Karpowicz, S. J., Prochnik, S. E., Grossman, A. R., & Merchant, S. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.233734 · Cited by 123 · see citing works

Transcriptome analysis of Chlamydomonas reinhardtii during the process of lipid accumulation

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Omics in algae: Paving the way for a systems biological understanding of algal stress phenomena?

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Overexpression of an exogenous phytoene synthase gene in the unicellular alga Chlamydomonas reinhardtii leads to an increase in the content of carotenoids

Couso, I., Vilà, M., Rodrı́guez, H., Vargas, M. A., & León, R. (2010) · Biotechnology Progress · doi:10.1002/btpr.527 · Cited by 118 · see citing works

Proteomic analysis of Chlorella vulgaris: Potential targets for enhanced lipid accumulation

Guarnieri, M. T., Nag, A., Yang, S., & Pienkos, P. T. (2013) · Journal of Proteomics · doi:10.1016/j.jprot.2013.05.025 · Cited by 113 · see citing works

System Response of Metabolic Networks in Chlamydomonas reinhardtii to Total Available Ammonium

Lee, D. Y., Park, J.-J., Barupal, D. K., & Fiehn, O. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.016733 · Cited by 103 · see citing works

Paths toward Algal Genomics

Grossman, A. R. (2005) · PLANT PHYSIOLOGY · doi:10.1104/pp.104.053447 · Cited by 99 · see citing works

Metabolic and cellular organization in evolutionarily diverse microalgae as related to biofuels production

Hildebrand, M., Abbriano, R. M., Polle, J. E. W., Traller, J. C., Trentacoste, E. M., Smith, S. R., & Davis, A. K. (2013) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2013.02.027 · Cited by 96 · see citing works

Recent advances on multidimensional liquid chromatography–mass spectrometry for proteomics: From qualitative to quantitative analysis—A review

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Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data

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Proteomics of model and crop plant species: Status, current limitations and strategic advances for crop improvement

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Production of anti‐cancer immunotoxins in algae: Ribosome inactivating proteins as fusion partners

Tran, M., Henry, R. E., Siefker, D. T., Van, C., Newkirk, G. M., Kim, J. J., Bui, J. D., & Mayfield, S. P. (2013) · Biotechnology and Bioengineering · doi:10.1002/bit.24966 · Cited by 79 · see citing works

Bio-crude transcriptomics: Gene discovery and metabolic network reconstruction for the biosynthesis of the terpenome of the hydrocarbon oil-producing green alga, Botryococcus braunii race B (Showa)*

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New insights into C hlamydomonas reinhardtii hydrogen production processes by combined microarray/ RNA ‐seq transcriptomics

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Functional Identification of Triterpene Methyltransferases from Botryococcus braunii Race B

Niehaus, T. D., Kinison, S., Okada, S., Yeo, Y., Bell, S. A., Cui, P., Devarenne, T. P., & Chappell, J. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.316059 · Cited by 54 · see citing works

Gene expression profile analysis in astaxanthin-induced Haematococcus pluvialis using a cDNA microarray

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The single cellular green microalga Botryococcus braunii, race B possesses three distinct 1-deoxy-d-xylulose 5-phosphate synthases

Matsushima, D., Jenke‐Kodama, H., Sato, Y., Fukunaga, Y., Sumimoto, K., Kuzuyama, T., Matsunaga, S., & Okada, S. (2012) · Plant Science · doi:10.1016/j.plantsci.2012.01.002 · Cited by 49 · see citing works

De novo transcriptomic analysis of hydrogen production in the green alga Chlamydomonas moewusii through RNA-Seq

Yang, S., Guarnieri, M. T., Smolinski, S. L., Ghirardi, M. L., & Pienkos, P. T. (2013) · Biotechnology for Biofuels · doi:10.1186/1754-6834-6-118 · Cited by 43 · see citing works

Global expression profiling of Chlamydomonas reinhardtii exposed to trace levels of free cadmium

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Transcriptome analysis of an oil-rich race A strain of Botryococcus braunii (BOT-88-2) by de novo assembly of pyrosequencing cDNA reads

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The microbial cell factory

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Coordinated Regulation of Gene Expression for Carotenoid Metabolism in Chlamydomonas reinhardtii

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The potential of photosynthetic aquatic species as sources of useful cellulose fibers—a review

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Transcriptome analysis of an oil-rich race B strain of Botryococcus braunii (BOT-22) by de novo assembly of pyrosequencing cDNA reads

Ioki, M., Baba, M., Nakajima, N., Shiraiwa, Y., & Watanabe, M. M. (2011) · Bioresource Technology · doi:10.1016/j.biortech.2011.08.104 · Cited by 27 · see citing works

Molecular and functional characterization of a cDNA encoding 4-hydroxy-3-methylbut-2-enyl diphosphate reductase from Dunaliella salina

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The metabolomics of carotenoids in engineered cell factory

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Differential gene expression of Chlamydomonas reinhardtii in response to 2,4,6-trinitrotoluene (TNT) using microarray analysis

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Transcriptome analysis of an oil-rich race B strain of Botryococcus braunii (BOT-70) by de novo assembly of 5′-end sequences of full-length cDNA clones

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Modes of hydrocarbon oil biosynthesis revealed by comparative gene expression analysis for race A and race B strains of Botryococcus braunii

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Green algae as a platform to express therapeutic proteins.

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Comparative proteomics lends insight into genotype‐specific pathogenicity

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Microalgae, old sustainable food and fashion nutraceuticals

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Manipulating environmental stresses and stress tolerance of microalgae for enhanced production of lipids and value-added products–a review

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Microalgae biofuels: illuminating the path to a sustainable future amidst challenges and opportunities

Wang, M., Ye, X., Bi, H., & Shen, Z. (2024) · Biotechnology for Biofuels and Bioproducts · doi:10.1186/s13068-024-02461-0 · Cited by 201 · see citing works

Stresses as First-Line Tools for Enhancing Lipid and Carotenoid Production in Microalgae

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The algal chloroplast as a synthetic biology platform for production of therapeutic proteins

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Green technology for the industrial production of biofuels and bioproducts from microalgae: A review

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Multiomics approaches and genetic engineering of metabolism for improved biorefinery and wastewater treatment in microalgae

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Experimental and Model-Based Analysis to Optimize Microalgal Biomass Productivity in a Pilot-Scale Tubular Photobioreactor

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An Insight into the Potential Application of Microalgae in Pharmaceutical and Nutraceutical Production

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Relationship Between the Period and Quantity of Algae Production and TN/TP in Water

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Introduction to Omics

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