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Engineering microalgae: transition from empirical design to programmable cells

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Improvement of biomass and lipid yield under stress conditions by using diploid strains of Chlamydomonas reinhardtii

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Unstable RNAi Effects Through Epigenetic Silencing of an Inverted Repeat Transgene in Chlamydomonas reinhardtii

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Improved and versatile viral 2 A platforms for dependable and inducible high‐level expression of dicistronic nuclear genes in C hlamydomonas reinhardtii

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Involvement of a Short Interspersed Element in Epigenetic Transcriptional Silencing of the Amoebapore Gene in Entamoeba histolytica

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Initiation of silencing of maize MuDR/Mu transposable elements

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SET3p monomethylates histone H3 on lysine 9 and is required for the silencing of tandemly repeated transgenes in Chlamydomonas

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Functional Specialization ofChlamydomonas reinhardtiiCytosolic Thioredoxin h1 in the Response to Alkylation-Induced DNA Damage

Sarkar, N., Lemaire, S. D., Wu‐Scharf, D., Issakidis‐Bourguet, E., & Cerutti, H. D. (2005) · Eukaryotic Cell · doi:10.1128/ec.4.2.262-273.2005 · Cited by 39 · see citing works

Development and characterization of a Nannochloropsis mutant with simultaneously enhanced growth and lipid production

Ryu, A. J., Kang, N. K., Jeon, S., Hur, D. H., Lee, E. M., Lee, D. Y., Jeong, B., Chang, Y. K., & Jeong, K. J. (2020) · Biotechnology for Biofuels · doi:10.1186/s13068-020-01681-4 · Cited by 38 · see citing works

Using Natural Selection to Explore the Adaptive Potential of Chlamydomonas reinhardtii

Perrineau, M., Gross, J., Zelzion, E., Price, D. C., Levitan, O., Boyd, J. M., & Bhattacharya, D. (2014) · PLoS ONE · doi:10.1371/journal.pone.0092533 · Cited by 38 · see citing works

The epigenetic origin of life history transitions in plants and algae

Vigneau, J., & Borg, M. (2021) · Plant Reproduction · doi:10.1007/s00497-021-00422-3 · Cited by 37 · see citing works

Heterologous overexpression of sfCherry fluorescent protein in Nannochloropsis salina

Kang, N. K., Choi, G., Kim, E. K., Shin, S.-E., Jeon, S., Park, M., Jeong, K. J., Jeong, B., Chang, Y. K., Yang, J.-W., et al. (2015) · Biotechnology Reports · doi:10.1016/j.btre.2015.08.004 · Cited by 36 · see citing works

A WD40‐repeat containing protein, similar to a fungal co‐repressor, is required for transcriptional gene silencing in Chlamydomonas

Zhang, C., Wu‐Scharf, D., Jeong, B., & Cerutti, H. D. (2002) · The Plant Journal · doi:10.1046/j.1365-313x.2002.01331.x · Cited by 36 · see citing works

Expanding the Molecular toolkit for Chlamydomonas reinhardtii – from History to new Frontiers

Fuhrmann, M. (2002) · Protist · doi:10.1078/14344610260450082 · Cited by 36 · see citing works

Safe-Harboring based novel genetic toolkit for Nannochloropsis salina CCMP1776: Efficient overexpression of transgene via CRISPR/Cas9-Mediated Knock-in at the transcriptional hotspot

Ryu, A. J., Jeong, B., Kang, N. K., Jeon, S., Sohn, M. G., Yun, H. J., Lim, J. M., Jeong, S. W., Park, Y., Jeong, W.-J., et al. (2021) · Bioresource Technology · doi:10.1016/j.biortech.2021.125676 · Cited by 35 · see citing works

In the Grip of Algal Genomics

Grossman, A. R. (2008) · Advances in experimental medicine and biology · doi:10.1007/978-0-387-75532-8_6 · Cited by 32 · see citing works

Transgenicism in algae: Challenges in compatibility, global scenario and future prospects for next generation biofuel production

Bharathiraja, B., Iyyappan, J., Gopinath, M., Jayamuthunagai, J., & Praveenkumar, R. (2021) · Renewable and Sustainable Energy Reviews · doi:10.1016/j.rser.2021.111829 · Cited by 31 · see citing works

kangaroo, a Mobile Element From Volvox carteri, Is a Member of a Newly Recognized Third Class of Retrotransposons

Duncan, L., Bouckaert, K., Yeh, F., & Kirk, D. L. (2002) · Genetics · doi:10.1093/genetics/162.4.1617 · Cited by 29 · see citing works

I elements in Drosophila: in vivo retrotransposition and regulation

Chambeyron, S., & Bucheton, A. (2005) · Cytogenetic and Genome Research · doi:10.1159/000084955 · Cited by 27 · see citing works

Natural History of Transposition in the Green Alga Chlamydomonas reinhardtii: Use of the AMT4 Locus as an Experimental System

Kim, K.-S., Kustu, S. G., & Inwood, W. B. (2006) · Genetics · doi:10.1534/genetics.106.058263 · Cited by 27 · see citing works

Complementation of a mutation in CpSRP43 causing partial truncation of light-harvesting chlorophyll antenna in Chlorella vulgaris

Shin, W.-S., Lee, B., Kang, N. K., Kim, Y., Jeong, W.-J., Kwon, J.-H., Jeong, B., & Chang, Y. K. (2017) · Scientific Reports · doi:10.1038/s41598-017-18221-0 · Cited by 25 · see citing works

Rates and spectra of de novo structural mutations in Chlamydomonas reinhardtiiPreprint

López‐Cortegano, E., Craig, R. J., Chebib, J., Balogun, E. J., & Keightley, P. D. (2022) · Genome Research · doi:10.1101/gr.276957.122 · Cited by 22 · see citing works

Inhibition of DNA Methylation in Picochlorum soloecismus Alters Algae Productivity

Steadman, C. R., Banerjee, S., Kunde, Y. A., Sanders, C. K., Marrone, B. L., & Twary, S. N. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.560444 · Cited by 24 · see citing works

Increasing lipid production in Chlamydomonas reinhardtii through genetic introduction for the overexpression of glyceraldehyde-3-phosphate dehydrogenase

Shin, S., Koh, H. G., Park, K., Park, S., Chang, Y. K., & Kang, N. K. (2024) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2024.1396127 · Cited by 22 · see citing works

Genetics and Biochemistry of RNAi in Drosophila

Kavi, H. H., Fernandez, H. R., Xie, W., & Birchler, J. A. (2007) · Current topics in microbiology and immunology · doi:10.1007/978-3-540-75157-1_3 · Cited by 22 · see citing works

Gene Silencing Triggered by Non-LTR Retrotransposons in the Female Germline of Drosophila melanogaster

Robin, S., Chambeyron, S., Bucheton, A., & Busseau, I. (2003) · Genetics · doi:10.1093/genetics/164.2.521 · Cited by 22 · see citing works

Ku80 Participates in the Targeting of Retroviral Transgenes to the Chromatin of CHO Cells

Masson, C., Bury-Moné, S., Guiot, E., Sáez-Cirión, A., Schoëvaërt-Brossault, D., Brachet-Ducos, C., Delelis, O., Subra, F., Jeanson-Leh, L., & Mouscadet, J. (2007) · Journal of Virology · doi:10.1128/jvi.02015-06 · Cited by 18 · see citing works

Optimization of electroporation-based multiple pulses and further improvement of transformation efficiency using bacterial conditioned medium for Nannochloropsis salina

Jeon, S., Kang, N. K., Suh, W. I., Koh, H. G., Lee, B., & Chang, Y. K. (2018) · Journal of Applied Phycology · doi:10.1007/s10811-018-1599-7 · Cited by 17 · see citing works

Nuclear proteome analysis of Chlamydomonas with response to CO2 limitation

Arias, C., Obudulu, O., Zhao, X., Ansolia, P., Zhang, X., Paul, S., Bygdell, J., Pirmoradian, M., Zubarev, R. A., Samuelsson, G. S., et al. (2020) · Algal Research · doi:10.1016/j.algal.2019.101765 · Cited by 15 · see citing works

Quantitative Proteomics and Phosphoproteomics Support a Role for Mut9-Like Kinases in Multiple Metabolic and Signaling Pathways in Arabidopsis

Wilson, M. E., Tzeng, S., Augustin, M. M., Meyer, M. R., Jiang, X., Choi, J. H., Rogers, J. C., Evans, B. S., Kutchan, T. M., & Nusinow, D. A. (2021) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2021.100063 · Cited by 15 · see citing works

Epigenetic Silencing of Gene Expression in Entamoeba histolytica

Mirelman, D., Anbar, M., Nuchamowitz, Y., & Bracha, R. (2005) · Archives of Medical Research · doi:10.1016/j.arcmed.2005.09.003 · Cited by 14 · see citing works

Genome editing of epigenetic transgene silencing in Chlamydomonas reinhardtii

Einhaus, A., Krieger, A., Köhne, L., Rautengarten, B., Jacobebbinghaus, N., Saudhof, M., Baier, T., & Kruse, O. (2025) · Trends in biotechnology · doi:10.1016/j.tibtech.2025.04.019 · Cited by 11 · see citing works

Tuning SAS-6 architecture with monobodies impairs distinct steps of centriole assembly

Hatzopoulos, G. N., Kükenshöner, T., Banterle, N., Favez, T., Flückiger, I., Hamel, V., Andany, S. H., Fantner, G. E., Hantschel, O. D., & Gönczy, P. (2021) · Nature Communications · doi:10.1038/s41467-021-23897-0 · Cited by 10 · see citing works

Studies on the effects of a flanking repetitive sequence on the expression of single-copy transgenes in Nicotiana sylvestris and in N. sylvestris-N. tomentosiformis hybrids

Kunz, C., Narangajavana, J., Jakowitsch, J., Park, Y.-D., Delon, T. R., Kovařı́k, A., Koukalová, B., van der Winden, J., Moscone, E., Aufsatz, W., et al. (2003) · Plant Molecular Biology · doi:10.1023/a:1023937006311 · Cited by 10 · see citing works

Small RNAs >26 nt in length associate with AGO1 and are upregulated by nutrient deprivation in the alga Chlamydomonas

Li, Y., Kim, E.-J., Voshall, A., Moriyama, E. N., & Cerutti, H. D. (2023) · The Plant Cell · doi:10.1093/plcell/koad093 · Cited by 9 · see citing works

Impacts of elevated CO2 on exogenous Bacillus thuringiensis toxins and transgene expression in transgenic rice under different levels of nitrogen

Jiang, S., Lu, Y., Dai, Y., Qian, L., Bodlah, M. A., Li, T., Wan, G., Parajulee, M. N., & Chen, F. (2017) · Scientific Reports · doi:10.1038/s41598-017-15321-9 · Cited by 9 · see citing works

Epigenetic Silencing of Transposons in the Green Alga Chlamydomonas reinhardtii

van Dijk, K., Xu, H., & Cerutti, H. D. (2006) · Nucleic acids and molecular biology · doi:10.1007/978-3-540-28130-6_8 · Cited by 9 · see citing works

Cell Biology: The Green Alga Chlamydomonas reinhardtii - A Genetic Model Organism

Nickelsen, J. (2005) · Springer eBooks · doi:10.1007/3-540-27043-4_4 · Cited by 8 · see citing works

Manipulation of Microalgal Lipid Production: A Genetic Engineering Aspect

Foo, S. C., Khong, N. M. H., & Yusoff, F. M. (2019) · Springer eBooks · doi:10.1007/978-981-13-2264-8_9 · Cited by 8 · see citing works

Epigenetics in Algae

Steadman, C. R. (2023) · doi:10.1002/9781119821946.ch17 · Cited by 8 · see citing works

PyMPV17, the MPV17 Homolog of Pyropia yezoensis (Rhodophyta), Enhances Osmotic Stress Tolerance in Chlamydomonas

Wi, J., Park, E., Hwang, M. S., Jeong, W.-J., & Choi, D. (2019) · Plant Molecular Biology Reporter · doi:10.1007/s11105-019-01172-3 · Cited by 7 · see citing works

A nuclear fucosyltransferase-like protein, PtFUT, from marine red alga Pyropia tenera (Rhodophyta) confers osmotic stress tolerance

Wi, J., Jung, H. S., Im, S., Yang, S., Park, E., Hwang, M. S., Jeong, W.-J., & Choi, D. (2017) · Journal of Applied Phycology · doi:10.1007/s10811-017-1241-0 · Cited by 7 · see citing works

A facile Agrobacterium-mediated transformation method for the model unicellular green algae Chlamydomonas reinhardtii

Quach, T. N., Sato, S. J., Behrens, M. R., Black, P. N., Dirusso, C., Cerutti, H. D., & Clemente, T. E. (2023) · In Vitro Cellular & Developmental Biology - Plant · doi:10.1007/s11627-023-10389-7 · Cited by 6 · see citing works

Engineering Microalgae: Transition from Empirical Design to Programmable Cells

Lu, Y., Zhang, X., Lin, H., & Melis, A. (2023) · CABI eBooks · doi:10.1079/9781800621954.0001 · Cited by 6 · see citing works

Epigenetic dynamics in Chlamydomonas: new frontiers in unicellular algal research

Carballo, J., Carbó, M., Pascual, J., Meijón, M., Álvarez, A., & Valledor, L. (2025) · Trends in Plant Science · doi:10.1016/j.tplants.2025.08.013 · Cited by 5 · see citing works

Identification and characterization of a heat shock transcription factor in the marine red alga Pyropia yezoensis (Rhodophyta)

Wi, J., & Choi, D. (2024) · Journal of Applied Phycology · doi:10.1007/s10811-024-03402-y · Cited by 4 · see citing works

Improved tolerance of recombinant Chlamydomonas rainhardtii with putative 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase from Pyropia yezoensis to nitrogen starvation

Park, S.-J., Ahn, J. W., & Choi, J. (2021) · The Journal of Microbiology · doi:10.1007/s12275-022-1491-7 · Cited by 4 · see citing works

Significance of carbohydrate pathway in the maximization of biofuel production in Botryococcus sp: A Brief Review

Abba, Z., Mohammad, F. Z., Matias‐Peralta, H. M., & Nimaya, M. M. (2020) · CLSU International Journal of Science and Technology · doi:10.22137/ijst.2020.v4n1.02 · Cited by 3 · see citing works

Rates and spectra of de novo structural mutation in Chlamydomonas reinhardtiiPreprint

López‐Cortegano, E., Craig, R. J., Chebib, J., Balogun, E. J., & Keightley, P. D. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.05.23.493040 · Cited by 3 · see citing works

Histone H3 Phosphorylation in Plants and Other Organisms

Moraes, I., & Casas-Mollano, J. A. (2014) · Springer eBooks · doi:10.1007/978-3-319-07971-4_4 · Cited by 2 · see citing works

Circadian Rhythms in the Algal World

Bagchi, A., Vasuja, D., & Chhajer, A. K. (2026) · Studies in Rhythm Engineering · doi:10.1007/978-981-95-3592-7_5 · Cited by 1 · see citing works

MAKING CHLAMYDOMONAS REINHARDTII A BETTER MODEL ORGANISM: TACKLING THE INEFFICIENCY OF NUCLEAR TRANSGENE EXPRESSION AND IMPROVING METHODS FOR THE GENERATION AND CHARACTERIZATION OF INSERTIONAL MUTANT LIBRARIES

Plucinak, T. M. (2013) · Lincoln (University of Nebraska) · Cited by 1 · see citing works

Gene Silencing and its Applications in Plants

Angaj, S., & Darvishani, S. (2011) · CRC Press eBooks · doi:10.1201/b10882-13

Characterization of botryococcus sp. And identification of carbohydrates metabolic related enzymes toward lipid production

Abba, Z. (2019) · UTHM Institutional Repository (Universiti Tun Hussein Onn Malaysia)

A novel class of long small RNAs associates with Argonaute1 and is up-regulated by nutrient deprivation in the alga ChlamydomonasPreprint

Li, Y., Kim, E., Voshall, A., Moriyama, E. N., & Cerutti, H. D. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.17.484771

References to Volume 1

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Genetically Modified (GM) Microalgae for Biofuel Production

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Identification and characterization of a heat shock transcription factor in the marine red alga Neopyropia yezoensis (Rhodophyta)Preprint

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Epigenetic Silencing of Transposons in the Green Alga Chlamydomonas reinhardtii

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An epigenetic gene silencing pathway selectively acting on transgenic DNA in the green alga Chlamydomonas

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A WD40‐repeat containing protein, similar to a fungal co‐repressor, is required for transcriptional gene silencing in Chlamydomonas

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