Publications

2024

Grau-Bové, X., Subirana, L., Meister, L., Soubigou, A., Neto, A., Elek, A., Fornas, O., Gomez-Skarmeta, J.L., Tena, J.J., Irimia, M., Bertrand, S., Sebé-Pedrós, A., Escriva, H., 2023. An amphioxus neurula stage cell atlas supports a complex scenario for the emergence of vertebrate head mesoderm. Nature Communications in press

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Robertson, H. E., Sebé-Pedrós, A., Saudemont, B., Loe Mie, Y., Zakrzewski, A., Grau-Bové, X., Mailhe, M.-P., Schiffer, P., Telford, M. J., & Marlow, H., 2024. Single cell atlas of Xenoturbella bocki highlights the limited cell-type complexity of a non-vertebrate deuterostome lineage. Nature Communications 15, 2469 (2024). [PDF] [link]

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Zolotarov, G., Grau-Bové, X., & Sebé-Pedrós, A. (2024). GeneExt: a gene model extension tool for enhanced single-cell RNA-seq analysis. BioRxiv, 2023.12.05.570120. https://doi.org/10.1101/2023.12.05.570120

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2023

Najle, S.R., Grau-Bové, X., Elek, A., Navarrete, C., Cianferoni, D., Chiva, C., Cañas-Armenteros, D., Mallabiabarrena, A., Kamm, K., Sabidó, E., Gruber-Vodicka, H., Schierwater, B., Serrano, L., Sebé-Pedrós, A., 2023. Stepwise emergence of the neuronal gene expression program in early animal evolution. Cell 186, 4676-4693.e29. [PDF] [link]

Cover article [link]

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Li, Y., Slavik, K.M., Toyoda, H.C., Morehouse, B.R., de Oliveira Mann, C.C., Elek, A., Levy, S., Wang, Z., Mears, K.S., Liu, J., Kashin, D., Guo, X., Mass, T., Sebé-Pedrós, A., Schwede, F., Kranzusch, P.J., 2023. cGLRs are a diverse family of pattern recognition receptors in innate immunity. Cell 186, 3261-3276.e20. [PDF] [link]

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2022

Miguel-Escalada, I., Maestro, M. Á., Balboa, D., Elek, A., Bernal, A., Bernardo, E., Grau, V., García-Hurtado, J., Sebé-Pedrós, A., & Ferrer, J., 2022. Pancreas agenesis mutations disrupt a lead enhancer controlling a developmental enhancer cluster. Developmental Cell 57(16), 1922-1936.e9 [PDF] [link]

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Grau-Bové, X., Navarrete, C., Chivas, C., Pribasnig, T., Antó, M., Torruella, G., Galindo, L.J., Lang, B.F., Moreira, D., López-Garcia, P., Ruiz-Trillo, I., Schleper, C., Sabidó, E. and Sebé-Pedrós, A., 2022. A phylogenetic and proteomic reconstruction of eukaryotic chromatin evolution. Nature Ecology and Evolution 6, 1007–1023 [PDF] [link]

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2021

Tanay, A., and Sebé-Pedrós, A., 2021. Evolutionary Cell Type Mapping with Single-Cell Genomics. Trends in Genetics. 37, 919–932. [PDF] [link]

 

Grau-Bové, X., and Sebé-Pedrós, A., 2021. Orthology clusters from gene trees with Possvm. Molecular Biology and Evolution 8, 5204–5208. [PDF] [link]

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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 185(11), 2973-2987.e18 [PDF] [link]

Cover article [link] and Preview [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]

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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]

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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]

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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]

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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]

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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]

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de Mendoza, A., Sebé-Pedrós, A., 2019. Origin and evolution of eukaryotic transcription factors. Curr. Opin. Genet. Dev. 59, 25–32. [PDF] [link]

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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. Nature Ecology and Evolution 2, 1176–1188. [PDF] [link]

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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]

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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]

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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]

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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]

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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]

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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]

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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]

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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]

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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]

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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]

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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]

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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]

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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]

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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]

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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]

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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]

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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]

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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]

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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]

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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]

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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]

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Sebé-Pedrós, A., Ruiz-Trillo, I., 2010. Integrin-mediated adhesion complex. Commun. Integr. Biol. 3, 475–477. [PDF] [link]

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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]

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