The Symbiomics Lab - Publications

Cui, Guoxin, Yi Jin Liew, Yong Li, Najeh Kharbatia, Noura I. Zahran, Abdul-Hamid Emwas, Victor M. Eguiluz, and Manuel Aranda. “Host-Dependent Nitrogen Recycling as a Mechanism of Symbiont Control in Aiptasia.” PLOS Genetics 15, no. 6 (June 24, 2019): e1008189. https://doi.org/10.1371/journal.pgen.1008189.

Keywords:

Nitrogen recycling, metabolomics, RNASeq, Host-symbiont relationship

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Ahmed, Hanin Ibrahim, Marcela Herrera, Yi Jin Liew, and Manuel Aranda. “Long-Term Temperature Stress in the Coral Model Aiptasia Supports the ‘Anna Karenina Principle’ for Bacterial Microbiomes.” Frontiers in Microbiology 10 (2019): 975. https://doi.org/10.3389/fmicb.2019.00975.

Keywords:

Anna Karenina principle, host-microbial partnerships, environmental stressors

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Chen, Jit Ern, Adrian C. Barbrook, Guoxin Cui, Christopher J. Howe, and Manuel Aranda. “The Genetic Intractability of Symbiodinium Microadriaticum to Standard Algal Transformation Methods.” PLOS ONE 14, no. 2 (February 19, 2019): e0211936. https://doi.org/10.1371/journal.pone.0211936.

Keywords:

Symbiodinium, Transformation methods, CRISPR/cas9

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Rädecker, Nils, Jit Ern Chen, Claudia Pogoreutz, Marcela Herrera, Manuel Aranda, and Christian R. Voolstra. “Nutrient Stress Arrests Tentacle Growth in the Coral Model Aiptasia.” Symbiosis, February 4, 2019. https://doi.org/10.1007/s13199-019-00603-9.

Keywords:

Nutrient stress, Exaiptasia, growth

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Cziesielski, Maha J., Yi Jin Liew, and Manuel Aranda. “Summarized Datasheet for Multi-Omics Response of Three Exaiptasia Strains to Heat Stress: A New Way to Process Omics Data.” BMC Research Notes 11, no. 1 (December 18, 2018): 905. https://doi.org/10.1186/s13104-018-4018-x.

Keywords:

Summarized datasheet, Aiptasia, Omics data

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Lehmann, Robert, Damien J. Lightfoot, Celia Schunter, Craig T. Michell, Hajime Ohyanagi, Katsuhiko Mineta, Sylvain Foret, et al. “Finding Nemo’s Genes: A Chromosome-Scale Reference Assembly of the Genome of the Orange Clownfish Amphiprion Percula.” Molecular Ecology Resources 0, no. 0 (September 10, 2018). https://doi.org/10.1111/1755-0998.12939.

Keywords:

Amphiprion percula, chromosome‐scale assembly, coral reef fish, fish genomics, functionalgenomics, Nemo, orange clownfish

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Li, Yong, Yi Jin Liew, Guoxin Cui, Maha J. Cziesielski, Noura Zahran, Craig T. Michell, Christian R. Voolstra, and Manuel Aranda. “DNA Methylation Regulates Transcriptional Homeostasis of Algal Endosymbiosis in the Coral Model Aiptasia.” Science Advances 4, no. 8 (August 1, 2018). https://doi.org/10.1126/sciadv.aat2142.

Keywords:

Cnidarians, dinoflagellates, symbiotic relationship, DNA methylation

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Liu, Huanle, Timothy G. Stephens, Raúl A. González-Pech, Victor H. Beltran, Bruno Lapeyre, Pim Bongaerts, Ira Cooke, et al. "Symbiodinium Genomes Reveal Adaptive Evolution of Functions Related to Coral-Dinoflagellate Symbiosis." Communications Biology 1, no. 1 (2018/07/17 2018): 95.

Keywords:

adaptive evolution, symbiodinium, coral-algal symbiosis, light stress

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Rädecker, Nils, Jean-Baptiste Raina, Mathieu Pernice, Gabriela Perna, Paul Guagliardo, Matt R. Kilburn, Manuel Aranda, and Christian R. Voolstra. "Using Aiptasia as a Model to Study Metabolic Interactions in Cnidarian-Symbiodinium Symbioses." Frontiers in Physiology 9 (2018): 214.

Keywords:

metaorganism, holobiont, carbon translocation, nitrogen uptake, Symbiodinium, selfish symbiont

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Cziesielski, M. J., Y. J. Liew, G. Cui, S. Schmidt-Roach, S. Campana, C. Marondedze, and M. Aranda. "Multi-Omics Analysis of Thermal Stress Response in a Zooxanthellate Cnidarian Reveals the Importance of Associating with Thermotolerant Symbionts." Proceedings of the Royal Society B: Biological Sciences 285, no. 1877 (2018).

Keywords:

transcriptomics, proteomics, heat stress, thermotolerance, Aiptasia, oxidative stress

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Liew, Yi Jin, Didier Zoccola, Yong Li, Eric Tambutté, Alexander A. Venn, Craig T. Michell, Guoxin Cui, et al. "Epigenome-Associated Phenotypic Acclimatization to Ocean Acidification in a Reef-Building Coral." Science Advances 4, no. 6 (2018).

Keywords:

Epigenome, Ocean acidification, Acclimatization

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DiBattista Joseph, D., Pablo Saenz-Agudelo, J. Piatek Marek, Xin Wang, Manuel Aranda, and L. Berumen Michael. "Using a Butterflyfish Genome as a General Tool for Rad-Seq Studies in Specialized Reef Fish." Molecular Ecology Resources 17, no. 6 (2017/11/01 2017): 1330-41.

Keywords:

adaptation,Chaetodontidae,ddRAD,ecologicalgenomics,next-generationsequencing,SNP

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Liew, Yi Jin, Yong Li, Sebastian Baumgarten, Christian R. Voolstra, and Manuel Aranda. "Condition-Specific Rna Editing in the Coral Symbiont Symbiodinium Microadriaticum." PLOS Genetics 13, no. 2 (2017): e1006619.

Keywords:

Symbiodinium, RNA editing, corals

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Voolstra, Christian R., Giga Community of Scientists, Gert Wörheide, and Jose V. Lopez. "Advancing Genomics through the Global Invertebrate Genomics Alliance (Giga)." Invertebrate systematics 31, no. 1 (03/16 2017): 1-7.

Keywords:

biodiversity, evolution, genetics, Metazoa.

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Herrera, Marcela, Maren Ziegler, Christian R. Voolstra, and Manuel Aranda. "Laboratory-Cultured Strains of the Sea Anemone Exaiptasia Reveal Distinct Bacterial Communities." Frontiers in Marine Science 4 (2017): 115.

Keywords:

16S rRNA gene, coral, core microbiome, host-specific, model organism

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Wang, Xin, Jin Liew Yi, Yong Li, Didier Zoccola, Sylvie Tambutte, and Manuel Aranda. "Draft Genomes of the Corallimorpharians Amplexidiscus Fenestrafer and Discosoma Sp." Molecular Ecology Resources 17, no. 6 (2017/11/01 2017): e187-e95.

Keywords:

Amplexidiscus fenestrafer, Corallimorpharia, Discosoma sp., naked corals

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Rädecker, Nils, Claudia Pogoreutz, Maren Ziegler, Ananya Ashok, M. Barreto Marcelle, Veronica Chaidez, G. B. Grupstra Carsten, et al. "Assessing the Effects of Iron Enrichment across Holobiont Compartments Reveals Reduced Microbial Nitrogen Fixation in the Red Sea Coral Pocillopora Verrucosa." Ecology and Evolution 7, no. 16 (2017/08/01 2017): 6614-21.

Keywords:

coral reefs, diazotroph, holobiont, nutrient limitation, Symbiodinium, symbiosis

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Brüwer, J. D., S. Agrawal, Y. J. Liew, M. Aranda, and C. R. Voolstra. "Association of Coral Algal Symbionts with a Diverse Viral Community Responsive to Heat Shock." BMC Microbiology 17, no. 1 (2017).

Keywords:

RNA-Seq, Transcriptomics, Virus, Symbiodinium, Coral reef, Heat shock, Climate change

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Torda, Gergely, Jennifer M. Donelson, Manuel Aranda, Daniel J. Barshis, Line Bay, Michael L. Berumen, David G. Bourne, et al. "Rapid Adaptive Responses to Climate Change in Corals." Nature Climate Change 7 (09/01/online 2017): 627.

Keywords:

Adaptive response, corals, climate change, Transgenerational plasticity

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Wang, Xin, Guénola Drillon, Taewoo Ryu, Christian R. Voolstra, and Manuel Aranda. "Genome-Based Analyses of Six Hexacorallian Species Reject the “Naked Coral” Hypothesis." Genome Biology and Evolution 9, no. 10 (2017): 2626-34.

Keywords:

naked corals, Scleractinia, Corallimorpharia, phylogenomics, evolution, calcification

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Gegner, Hagen M., Maren Ziegler, Nils Rädecker, Carol Buitrago-López, Manuel Aranda, and Christian R. Voolstra. "High Salinity Conveys Thermotolerance in the Coral Model Aiptasia." Biology Open 6, no. 12 (2017): 1943.

Keywords:

Coral reefs, Climate change, Symbiosis, Thermotolerance, Resilience, Symbiodinium, Bleaching, Heat stress

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Voolstra, Christian R., Yong Li, Yi Jin Liew, Sebastian Baumgarten, Didier Zoccola, Jean-François Flot, Sylvie Tambutté, Denis Allemand, and Manuel Aranda. "Comparative Analysis of the Genomes of Stylophora Pistillata and Acropora Digitifera Provides Evidence for Extensive Differences between Species of Corals." Scientific Reports 7, no. 1 (2017/12/14 2017): 17583.

Keywords:

Stylophora, Acropora, Comparative genomics

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Baumgarten, Sebastian, J. Cziesielski Maha, Ludivine Thomas, T. Michell Craig, Y. Esherick Lisl, R. Pringle John, Manuel Aranda, and R. Voolstra Christian. "Evidence for Mirna-Mediated Modulation of the Host Transcriptome in Cnidarian–Dinoflagellate Symbiosis." Molecular Ecology 27, no. 2 (2018/01/01 2017): 403-18.

Keywords:

Aiptasia anemone Argonaute coral cross-linking immunoprecipitation

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Chen, Jit Ern, Guoxin Cui, Xin Wang, Yi Jin Liew, and Manuel Aranda. "Recent Expansion of Heat-Activated Retrotransposons in the Coral Symbiont Symbiodinium Microadriaticum." The ISME Journal 12 (10/20/online 2017): 639.

Keywords:

Retrotransposon, Symbiodinium, Expansion events

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Ryu, Taewoo, Loqmane Seridi, Lucas Moitinho-Silva, Matthew Oates, Yi Jin Liew, Charalampos Mavromatis, Xiaolei Wang, et al. "Hologenome Analysis of Two Marine Sponges with Different Microbiomes." BMC Genomics 17, no. 1 (2016/02/29 2016): 158.

Keywords:

Sponge, Stylissa carteri, Xestospongia testudinaria, Innate immune system, Host-Microbial symbionts, Hologenome

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Liew, Yi Jin, Taewoo Ryu, Manuel Aranda, and Timothy Ravasi. "Mirna Repertoires of Demosponges Stylissa Carteri and Xestospongia Testudinaria." PLOS ONE 11, no. 2 (2016): e0149080.

Keywords:

miRNA, sponges, biogenesis

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Bhattacharya, Debashish, Shobhit Agrawal, Manuel Aranda, Sebastian Baumgarten, Mahdi Belcaid, Jeana L. Drake, Douglas Erwin, et al. "Comparative Genomics Explains the Evolutionary Success of Reef-Forming Corals." eLife 5 (2016/05/24 2016): e13288.

Keywords:

corals, biomineralization, stress response, symbiotsis, horizontal gene transfer

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DiBattista Joseph, D., Xin Wang, Pablo Saenz-Agudelo, J. Piatek Marek, Manuel Aranda, and L. Berumen Michael. "Draft Genome of an Iconic Red Sea Reef Fish, the Blacktail Butterflyfish (Chaetodon Austriacus): Current Status and Its Characteristics." Molecular Ecology Resources 18, no. 2 (2018/03/01 2016): 347-55.

Keywords:

DiBattista Joseph D., Wang Xin, Saenz-Agudelo Pablo, Piatek Marek J., Aranda Manuel, Berumen Michael L.

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Liew, Yi Jin, Manuel Aranda, and Christian R. Voolstra. "Reefgenomics.Org - a Repository for Marine Genomics Data." Database (2016): baw152-baw52.

Keywords:

repository, database, website

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Aranda, M., Y. Li, Y. J. Liew, S. Baumgarten, O. Simakov, M. C. Wilson, J. Piel, et al. "Genomes of Coral Dinoflagellate Symbionts Highlight Evolutionary Adaptations Conducive to a Symbiotic Lifestyle." Scientific Reports 6 (12/22/online 2016): 39734.

Keywords:

dinoflagellate symbionts, adaptation, comparative genomics

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Röthig, Till, Rúben M. Costa, Fabia Simona, Sebastian Baumgarten, Ana F. Torres, Anand Radhakrishnan, Manuel Aranda, and Christian R. Voolstra. "Distinct Bacterial Communities Associated with the Coral Model Aiptasia in Aposymbiotic and Symbiotic States with Symbiodinium." Frontiers in Marine Science 3 (2016): 234.

Keywords:

coral reef, cnidarian-dinoflagellate symbiosis, microbial community profiling, 16S rRNA gene, functional profiling

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Ganot, Philippe, Didier Zoccola, Eric Tambutté, Christian R. Voolstra, Manuel Aranda, Denis Allemand, and Sylvie Tambutté. "Structural Molecular Components of Septate Junctions in Cnidarians Point to the Origin of Epithelial Junctions in Eukaryotes." Molecular Biology and Evolution 32, no. 1 (2015): 44-62.

Keywords:

Epitheliozoa, Claudin, Neurexin, Contactin, Neuroglian, Coracle, MAGUK, Na+/K+ ATPase transporter, DSCAM, Nbl4, para-cellular pathway, permselectivity, corals, ctenophores, poriferans, Monosiga, Capsaspora

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Zoccola, Didier, Philippe Ganot, Anthony Bertucci, Natacha Caminiti-Segonds, Nathalie Techer, Christian R. Voolstra, Manuel Aranda, et al. "Bicarbonate Transporters in Corals Point Towards a Key Step in the Evolution of Cnidarian Calcification." Scientific Reports 5 (06/04/online 2015): 9983.

Keywords:

biocarbonate transporters, calcification, Stylophora

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Roder, Cornelia, Till Bayer, Manuel Aranda, Maren Kruse, and R. Voolstra Christian. "Microbiome Structure of the Fungid Coral Ctenactis Echinata Aligns with Environmental Differences." Molecular Ecology 24, no. 13 (2015/07/01 2015): 3501-11.

Keywords:

coral reef, ecological niche, holobiont, metaorganism, microbiome, symbiosis

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Baumgarten, S., O. Simakov, L. Y. Esherick, Y. J. Liew, E. M. Lehnert, C. T. Michell, Y. Li, et al. "The Genome of Aiptasia, a Sea Anemone Model for Coral Symbiosis." Proceedings of the National Academy of Sciences of the United States of America 112, no. 38 (2015): 11893-98.

Keywords:

coral reefs, endosymbiosis, horizontal gene transfer, dinoflagellate, pattern-recognition receptors

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Liew, Yi Jin, Manuel Aranda, Adrian Carr, Sebastian Baumgarten, Didier Zoccola, Sylvie Tambutté, Denis Allemand, Gos Micklem, and Christian R. Voolstra. "Identification of Micrornas in the Coral Stylophora Pistillata." PLOS ONE 9, no. 3 (2014): e91101.

Keywords:

miRNA, coral calcification, symbiosis

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Bayer, T., C. Arif, C. Ferrier-Pagès, D. Zoccola, M. Aranda, and C. R. Voolstra. "Bacteria of the Genus Endozoicomonas Dominate the Microbiome of the Mediterranean Gorgonian Coral Eunicella Cavolini." Marine Ecology Progress Series 479 (2013): 75-84.

Keywords:

Microbial communities, Gorgonian, Eunicella cavolini, 16S tag sequencing

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Jessen, Christian, Javier Felipe Villa Lizcano, Till Bayer, Cornelia Roder, Manuel Aranda, Christian Wild, and Christian R. Voolstra. "In-Situ Effects of Eutrophication and Overfishing on Physiology and Bacterial Diversity of the Red Sea Coral Acropora Hemprichii." PLOS ONE 8, no. 4 (2013): e62091.

Keywords:

16S based, bacterial community, eutrophication

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Bayer, Till, Matthew J. Neave, Areej Alsheikh-Hussain, Manuel Aranda, Lauren K. Yum, Tracy Mincer, Konrad Hughen, Amy Apprill, and Christian R. Voolstra. "The Microbiome of the Red Sea Coral Stylophora Pistillata Is Dominated by Tissue-Associated Endozoicomonas Bacteria." Applied and environmental microbiology 79, no. 15 (2013): 4759-62.

Keywords:

coral, endozoicomonas, phylogeny

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Roder, Cornelia, Chatchanit Arif, Till Bayer, Manuel Aranda, Camille Daniels, Ahmed Shibl, Suchana Chavanich, and Christian R. Voolstra. "Bacterial Profiling of White Plague Disease in a Comparative Coral Species Framework." The ISME Journal 8 (08/08/online 2013): 31.

Keywords:

16S rRNA gene microarray, Gulf of Thailand, Pavona duerdeni, Porites lutea, coral disease, White Plague Disease (WPD)

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Baumgarten, Sebastian, Till Bayer, Manuel Aranda, Yi Jin Liew, Adrian Carr, Gos Micklem, and Christian R. Voolstra. "Integrating Microrna and Mrna Expression Profiling in Symbiodinium Microadriaticum, a Dinoflagellate Symbiont of Reef-Building Corals." BMC genomics 14, no. 1 (2013): 704.

Keywords:

Symbiodinium Dinoflagellates, Scleractinian corals, Symbiont, Coral reef, Small RNA (smRNA), microRNA (miRNA), Small interfering RNA (siRNA), mRNA, Expression profiling, RNAseq

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Bayer, T., M. Aranda, S. Sunagawa, L. K. Yum, M. K. DeSalvo, E. Lindquist, M. A. Coffroth, C. R. Voolstra, and M. Medina. "Symbiodinium Transcriptomes: Genome Insights into the Dinoflagellate Symbionts of Reef-Building Corals." PLOS ONE 7, no. 4 (2012).

Keywords:

Symbiodinium, transcriptome, transcription factors

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Aranda, Manuel, Michael K. DeSalvo, Till Bayer, Monica Medina, and Christian R. Voolstra. "Evolutionary Insights into Scleractinian Corals Using Comparative Genomic Hybridizations." BMC Genomics 13:501-01

Keywords:

Coral reefs, Comparative genomic hybridization (CGH), Microarray, Mitochondria, Evolution

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Voolstra, Sunagawa, Matz, Bayer, Aranda, Buschiazzo, DeSalvo, Lindquist, Szmant, Coffroth and Medina, “Rapid Evolution of Coral Proteins Responsible for Interaction with the Environment,” PLOS ONE 6, no. 5 (2011).

Keywords:

Evolution, Coral, Interaction

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Aranda, Banaszak Anastazia, Bayer, Luyten James, Medina and Voolstra Christian, “Differential sensitivity of coral larvae to natural levels of ultraviolet radiation during the onset of larval competence,” Molecular Ecology 20, no. 14 (2011).

Keywords:

development, gene expression, global climate change, neurogenesis, stress response, ultraviolet radiation

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Ichim-Moreno, Aranda and Voolstra, “Identification of a gene expression core signature for Duchenne muscular dystrophy (DMD) via integrative analysis reveals novel potential compounds for treatment”. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (2010).

Keywords:

biocomputing, muscle, DMD, Duchenne muscular dystrophy, gene expression core signature identification, genetic disorders, integrative analysis reveals novel potential compounds, muscle degeneration, Calcium, Cardiac disease, Degenerative diseases, Drugs,

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Marques-Souza, Aranda and Tautz, “Delimiting the conserved features of hunchback function for the trunk organization of insects,” Development 135, no. 5 (2008).

Keywords:

Gap gene hunchback, Drosophila acts

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Tribolium Genome Sequencing, “The genome of the model beetle and pest Tribolium castaneum,” Nature 452(2008).

Keywords:

https://www.nature.com/articles/nature06784

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Aranda, Marques-Souza, Bayer and Tautz, “The role of the segmentation gene hairy in Tribolium,” Development Genes and Evolution 218, no. 9 (2008).

Keywords:

Segementation gene, Tribolium

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McGregor, Pechmann, Schwager, Feitosa, Kruck, Aranda and Damen, “Wnt8 Is Required for Growth-Zone Establishment and Development of Opisthosomal Segments in a Spider,” Current Biology 18, no. 20 (2008).

Keywords:

DEVBIO, EVO_ECOL

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Savard, Marques-Souza, Aranda and Tautz, “A Segmentation Gene in Tribolium Produces a Polycistronic mRNA that Codes for Multiple Conserved Peptides,” Cell 126, no. 3 (2006).

Keywords:

Segmentation genes, Tribolium, Polycistronic mRNA

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Beermann, Aranda and Schröder, “The Sp8 zinc-finger transcription factor is involved in allometric growth of the limbs in the beetle Tribolium castaneum,” Development 131, no. 4 (2004).

Keywords:

Tribolium Sp8, Leg elongation, Allometric growth, Serrate

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Eckert, Aranda, Wolff and Tautz, “Separable stripe enhancer elements for the pair-rule gene hairy in the beetle Tribolium,” EMBO Reports 5, no. 6 (2004).

Keywords:

segmentation, short germ-band development, gap genes, insects, germline transformation, reporter gene constructs

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Aranda, Kanellopoulou, Christ, Peitz, Rajewsky and Dröge, “Altered directionality in the cre-loxP site-specific recombination pathway11Edited by M. Yaniv,” Journal of Molecular Biology 311, no. 3 (2001).

Keywords:

Cre , site alignment , site-specific recombination , strand exchange , synaptic complex

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