Evolution of Cell Type Regulation
Evolution of Cell Type Regulation
Publications
A stony coral cell atlas illuminates the molecular and cellular basis of
coral symbiosis, calcification, and immunity
Over 40 cell types across the life cycle of Stylophora pistillata, a stony coral, are identified through the use of single-cell RNA sequencing. From this reference atlas, the molecular pathways underpinning coral reef building, specialized immune cells, and the metabolic programs involved in symbiosis between coral and algae partners are described.
2021
Tanay, A., and Sebé-Pedrós, A., 2021. Evolutionary Cell Type Mapping with Single-Cell Genomics. Trends in Genetics. DOI: 10.1016/j.tig.2021.04.008 [PDF] [link]
Grau-Bové, X., and Sebé-Pedrós, A., 2021. Orthology clusters from gene trees with Possvm. bioRxiv
DOI: 10.1101/2021.05.03.442399 [link]
Levy, S., Elek, A., Grau-Bové, X., Menéndez-Bravo, S., Iglesias, M., Tanay, A., Mass, T., A. Sebé-Pedrós A., 2021. A stony coral cell atlas illuminates the molecular and cellular basis of coral symbiosis, calcification, and immunity. Cell, 1–15 [PDF] [link]
García-Castro, H., Kenny, N., Iglesias, M., Álvarez-Campos, P., Mason, V., Schönauer, A., Sleight, V., Neiro, J., Aboobaker, A., Permanyer, J., Irimia, M., Sebé-Pedrós, A., Solana, J., 2021. ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics. Genome Biology 1–28. [PDF] [link]
2020
Ku, C., Sheyn, U., Sebé-Pedrós, A., Ben-Dor, S., Schatz, D., Tanay, A., Rosenwasser, S., Vardi, A., 2020. A single-cell view on alga-virus interactions reveals sequential transcriptional programs and infection states. Sci. Adv. 6, eaba4137. [PDF] [link]
Levy, S., Brekhman, V., Bakhman, A., Malik, A., Sebé-Pedrós, A., Kosloff, M., Lotan, T., 2020. Ectopic activation of GABAB receptors inhibits neurogenesis and metamorphosis in the cnidarian Nematostella vectensis. Nat. Ecol. Evol. [PDF] [link]
Peligero-Cruz, C., Givony, T., Sebé-Pedrós, A., Dobeš, J., Kadouri, N., Nevo, S., Roncato, F., Alon, R., Goldfarb, Y., Abramson, J., 2020. IL18 signaling promotes homing of mature Tregs into the thymus. Elife 9, 1–23. [PDF] [link]
2019
Ku, C., Sebé-Pedrós, A., 2019. Using single-cell transcriptomics to understand functional states and interactions in microbial eukaryotes. Philos. Trans. R. Soc. B Biol. Sci. 374, 20190098. [PDF] [link]
Baran, Y., Bercovich, A., Sebé-Pedrós, A., Lubling, Y., Giladi, A., Chomsky, E., Meir, Z., Hoichman, M., Lifshitz, A., Tanay, A., 2019. MetaCell: analysis of single-cell RNA-seq data using K-nn graph partitions. Genome Biol. 20, 206. [PDF] [link]
de Mendoza, A., Sebé-Pedrós, A., 2019. Origin and evolution of eukaryotic transcription factors. Curr. Opin. Genet. Dev. 59, 25–32. [PDF] [link]
2018
Sebé-Pedrós, A., Chomsky, E., Pang, K., Lara-Astiaso, D., Gaiti, F., Mukamel, Z., Amit, I., Hejnol, A., Degnan, B.M., Tanay, A., 2018. Early metazoan cell type diversity and the evolution of multicellular gene regulation. Nat. Ecol. Evol. 2, 1176–1188. [PDF] [link]
Sebé-Pedrós, A., Saudemont, B., Chomsky, E., Plessier, F., Mailhé, M.-P., Renno, J., Loe-Mie, Y., Lifshitz, A., Mukamel, Z., Schmutz, S., Novault, S., Steinmetz, P.R.H., Spitz, F., Tanay, A., Marlow, H., 2018. Cnidarian Cell Type Diversity and Regulation Revealed by Whole-Organism Single-Cell RNA-Seq. Cell 173, 1520-1534.e20. [PDF] [link]
Torruella, G., Grau-Bové, X., Moreira, D., Karpov, S.A., Burns, J.A., Sebé-Pedrós, A., Völcker, E., López-García, P., 2018. Global transcriptome analysis of the aphelid Paraphelidium tribonemae supports the phagotrophic origin of fungi. Commun. Biol. 1, 231. [PDF] [link]
Leonard, G., Labarre, A., Milner, D.S., Monier, A., Soanes, D., Wideman, J.G., Maguire, F., Stevens, S., Sain, D., Grau-Bové, X., Sebé-Pedrós, A., Stajich, J.E., Paszkiewicz, K., Brown, M.W., Hall, N., Wickstead, B., Richards, T.A., 2018. Comparative genomic analysis of the ‘pseudofungus’ Hyphochytrium catenoides. Open Biol. 8, 170184. [PDF] [link]
2017
Sebé-Pedrós, A., Ruiz-Trillo, I., 2017. Evolution and Classification of the T-Box Transcription Factor Family. Curr. Top. Dev. Biol. 122, 1–26. [PDF] [link]
Sebé-Pedrós, A., Degnan, B.M., Ruiz-Trillo, I., 2017. The origin of Metazoa: a unicellular perspective. Nat. Rev. Genet. 18, 498–512. [PDF] [link]
2016
Sebé-Pedrós, A., Ballaré, C., Parra-Acero, H., Chiva, C., Tena, J.J., Sabidó, E., Gómez-Skarmeta, J.L., Di Croce, L., Ruiz-Trillo, I., 2016. The Dynamic Regulatory Genome of Capsaspora and the Origin of Animal Multicellularity. Cell 165, 1224–1237. [PDF] [link]
Sebé-Pedrós, A., Peña, M.I., Capella-Gutiérrez, S., Antó, M., Gabaldón, T., Ruiz-Trillo, I., Sabidó, E., 2016. High-Throughput Proteomics Reveals the Unicellular Roots of Animal Phosphosignaling and Cell Differentiation. Dev. Cell 39, 186–197. [PDF] [link]
Before 2016
Alzayady, K.J., Sebé-Pedrós, A., Chandrasekhar, R., Wang, L., Ruiz-Trillo, I., Yule, D.I., 2015. Tracing the Evolutionary History of Inositol, 1, 4, 5-Trisphosphate Receptor: Insights from Analyses of Capsaspora owczarzaki Ca 2+ Release Channel Orthologs. Mol. Biol. Evol. 32, 2236–2253. [PDF] [link]
Grau-Bové, X., Sebé-Pedrós, A., Ruiz-Trillo, I., 2015. The Eukaryotic Ancestor Had a Complex Ubiquitin Signaling System of Archaeal Origin. Mol. Biol. Evol. 32, 726–739. [PDF] [link]
Sebé-Pedrós, A., de Mendoza, A., 2015. Transcription Factors and the Origin of Animal Multicellularity. In: Ruiz-Trillo, I., Nedelcu, A.M. (Eds.), Evolutionary Transitions to Multicellular Life, Advances in Marine Genomics. Springer Netherlands, Dordrecht, pp. 379–394. [PDF] [link]
Sebé-Pedrós, A., Grau-Bové, X., Richards, T. a, Ruiz-Trillo, I., 2014. Evolution and Classification of Myosins, a Paneukaryotic Whole-Genome Approach. Genome Biol. Evol. 6, 290–305. [PDF] [link]
de Mendoza, A., Sebé-Pedrós, A., Ruiz-Trillo, I., 2014. The Evolution of the GPCR Signaling System in Eukaryotes: Modularity, Conservation, and the Transition to Metazoan Multicellularity. Genome Biol. Evol. 6, 606–619. [PDF] [link]
Sebé-Pedrós, A., Ariza-Cosano, A., Weirauch, M.T., Leininger, S., Yang, A., Torruella, G., Adamski, M., Adamska, M., Hughes, T.R., Gomez-Skarmeta, J.L., Ruiz-Trillo, I., 2013. Early evolution of the T-box transcription factor family. Proc. Natl. Acad. Sci. 110, 16050–16055. [PDF] [link]
de Mendoza, A., Sebe-Pedros, A., Sestak, M.S., Matejcic, M., Torruella, G., Domazet-Loso, T., Ruiz-Trillo, I., 2013. Transcription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineages. Proc. Natl. Acad. Sci. 110, E4858–E4866. [PDF] [link]
Sebé-Pedrós, A., Burkhardt, P., Sánchez-Pons, N., Fairclough, S.R., Lang, B.F., King, N., Ruiz-Trillo, I., 2013. Insights into the Origin of Metazoan Filopodia and Microvilli. Mol. Biol. Evol. 30, 2013–2023. [PDF] [link]
Sebé-Pedrós, A., Irimia, M., del Campo, J., Parra-Acero, H., Russ, C., Nusbaum, C., Blencowe, B.J., Ruiz-Trillo, I., 2013. Regulated aggregative multicellularity in a close unicellular relative of metazoa. Elife 2, e01287–e01287. [PDF] [link]
Martín-Durán, J.M., de Mendoza, A., Sebé-Pedrós, A., Ruiz-Trillo, I., Hejnol, A., 2013. A broad genomic survey reveals multiple origins and frequent losses in the evolution of respiratory hemerythrins and hemocyanins. Genome Biol. Evol. 5, 1435–42. [PDF] [link]
Suga, H., Chen, Z., de Mendoza, A., Sebé-Pedrós, A., Brown, M.W., Kramer, E., Carr, M., Kerner, P., Vervoort, M., Sánchez-Pons, N., Torruella, G., Derelle, R., Manning, G., Lang, B.F., Russ, C., Haas, B.J., Roger, A.J., Nusbaum, C., Ruiz-Trillo, I., 2013. The Capsaspora genome reveals a complex unicellular prehistory of animals. Nat. Commun. 4, 1–9. [PDF] [link]
Grau-Bové, X., Sebé-Pedrós, A., Ruiz-Trillo, I., 2013. A Genomic Survey of HECT Ubiquitin Ligases in Eukaryotes Reveals Independent Expansions of the HECT System in Several Lineages. Genome Biol. Evol. 5, 833–847. [PDF] [link]
Sebé-Pedrós, A., Zheng, Y., Ruiz-Trillo, I., Pan, D., 2012. Premetazoan Origin of the Hippo Signaling Pathway. Cell Rep. 1, 13–20. [PDF] [link]
Sebé-Pedrós, A., de Mendoza, A., Lang, B.F., Degnan, B.M., Ruiz-Trillo, I., 2011. Unexpected repertoire of metazoan transcription factors in the unicellular holozoan Capsaspora owczarzaki. Mol. Biol. Evol. 28, 1241–54. [PDF] [link]
Sebé-Pedrós, A., Ruiz-Trillo, I., 2010. Integrin-mediated adhesion complex. Commun. Integr. Biol. 3, 475–477. [PDF] [link]
Sebé-Pedrós, A., Roger, A.J., Lang, F.B., King, N., Ruiz-Trillo, I., 2010. Ancient origin of the integrin-mediated adhesion and signaling machinery. Proc. Natl. Acad. Sci. 107, 10142–10147. [PDF] [link]