2025

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Maria Rossello, Sophie Tandonnet, Isabel Almudi. BarQC: Quality Control and Preprocessing for SPLiT-Seq Data BioRxiv doi: https://doi.org/10.1101/2025.02.04.635005 

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Torres-Oliva, M, Buchberger E, Buffry AD, Kittelmann M, Sumner-Rooney L, Gaspar P, Bullinger G. C., Guerrero G., Casares F, Arif S, Posnien N, Nunes MDS, McGregor AP & Almudi I. Heterochrony in orthodenticle expression is associated with ommatidial size variation between Drosophila species. BMC Biology 23, 34 (2025). https://doi.org/10.1186/s12915-025-02136-8

 

 

2024

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Carlos A. Martín-Blanco, Pablo Navarro, José Esteban-Collado, Florenci Serras, Isabel Almudi, Fernando Casares. Gill regeneration in the mayfly Cloeon uncovers new molecular pathways in insect regeneration  Open Biology, 14, 240118. https://doi.org/10.1098/rsob.240118

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Joan Pallares-Albanell, Laia Ortega-Flores, Tot Senar-Serra, Antoni Ruiz, Josep F Abril, Maria Rossello, Isabel Almudi. Gene regulatory dynamics during the development of a paleopteran insect, the mayfly Cloeon dipterum Development dev.203017.

https://doi.org/10.1242/dev.203017

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Katja M. Hoedjes, Sonja Grath, Nico Posnien, Michael G. Ritchie, Christian Schlötterer, Jessica K. Abbott, Isabel Almudi, Marta Coronado-Zamora, Esra Durmaz Mitchell, Thomas Flatt, Claudia Fricke, Amanda Glaser-Schmitt, Josefa González, Luke Holman, Maaria Kankare, Benedict Lenhart, Dorcas J. Orengo, Rhonda R. Snook, Vera M. Yılmaz, Leeban Yusuf.  From whole bodies to single cells: A guide to transcriptomic approaches for ecology and evolutionary biology. Molecular Ecology, 00, e17382. https://doi.org/10.1111/mec.17382

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Federica Mantica, Luis P. Iñiguez, Yamile Marquez, Jon Permanyer, Antonio Torres-Mendez, Josefa Cruz, Xavi Franch-Marro, Frank Tulenko, Demian Burguera, Stephanie Bertrand, Toby Doyle, Marcela Nouzova, Peter Currie, Fernando G. Noriega, Hector Escriva, Maria Ina Arnone, Caroline B Albertin, Karl R Wotton, Isabel Almudi, David Martin, Manuel Irimia. Pervasive evolution of tissue-specificity of ancestral genes differentially shaped vertebrates and insects Nature Ecology and Evolution (2024) https://doi.org/10.1038/s41559-024-02398-5

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2023

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Sara Molina-Gil, Sol Sotillos, José Manuel Espinosa-Vázquez, Isabel Almudi & James C.-G. Hombría. Interlocking of co-opted developmental gene networks in Drosophila and the evolution of pre-adaptive novelty. Nature communications 14, 5730 (2023)

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Kathrin Theissinger, Carlos Fernandes, et al., How genomics can help biodiversity conservation. Trends in Genetics, February 2023

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2022

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Torres-Mendez, A., Pop, S., Bonnal, S., Almudi, I., Roberts, R.J.V., Paolantoni, C., Alcaina, A., Avola, A., Martin Anduaga, A., Haussmann, I.H., Morin, V., Casares, F., Soller, M., Kadener, S., Roignant, J.-Y., Prieto-Godino, L., Irimia, M., 2022. Parallel evolution of a splicing program controlling neuronal excitability in flies and mammals. Science Advances, 8, eabk0445

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Giulio Formenti, Kathrin Theissinger, et al., The era of reference genomes in conservation genomics. Trends in Ecology & Evolution, March 2022, Vol. 37, No. 3

 

 

2021

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Orathai Kamsoi, Alba Ventos-Alfonso, Fernando Casares, Isabel Almudi, Xavier Belles. Regulation of metamorphosis in neopteran insects is conserved in the paleopteran Cloeon dipterum (Ephemeroptera) Proceedings of the National Aacademy of Sciences 021 118 (34) e2105272118

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Sofia J. Araújo, Isabel Almudi, Laura Bozal-Basterra, Fernando Casares, Sergio Casas-Tintó, Augusto Escalante, Fernando García-Moreno, María Losada-Pérez, Ignacio Maeso, Luciano Marcon, Oscar Ocaña, Olatz Pampliega, Álvaro Rada-Iglesias, Teresa Rayon, James Sharpe, James D. Sutherland, Cristina Villa del Campo and Rosa Barrio. Meeting report of the 17th Spanish Society for Developmental Biology Meeting (SEBD2020). International Journal of Developmental Biology. Jan 22.

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Buchberger, E., Bilen, A., Ayaz, S., Salamanca, D., Matas de las Heras, C., Niksic, A., Almudi, I., Torres-Oliva, M., Casares, F., Posnien, N. Variation in a pleiotropic hub gene drives morphological evolution: Insights from interspecific differences in head shape and eye size in Drosophila. Molecular Biology and Evolution, msaa335

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2020

 

Almudi, I.#., Vizueta, J., Wyatt, C.D.R., de Mendoza, A., Marletaz, F., Firbas, P.N., Feuda, R., Masiero, G., Medina, P., Alcaina-Caro, A., Cruz, F., Gomez-Garrido, J., Gut, M., Alioto, T.S., Vargas-Chavez, C., Davie, K., Misof, B., Gonzalez, J., Aerts, S., Lister, R., Paps, J., Rozas, J., Sanchez-Gracia, A., Irimia, M., Maeso, I., Casares, F.#., 2020. Genomic adaptations to aquatic and aerial life in mayflies and the origin of insect wings. Nature Communications 11, 2631.

 

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Ruiz-Sobrino, A.*, Martín-Blanco, C.A.*, Navarro, T.*, Almudí, I., Masiero, G., Jiménez-Caballero, M., Buchwalter, D.B., Funk, D.H., Gattolliat, J.L., Lemos, M.C., Jiménez, F., Casares, F., 2020. Space colonization by branching trachea explains the morphospace of a simple respiratory organ. Developmental Biology 462, 50-59.

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2019

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Almudi, I.#., Martin-Blanco, C.A., Garcia-Fernandez, I.M., Lopez-Catalina, A., Davie, K., Aerts, S., Casares, F.#., 2019. Establishment of the mayfly Cloeon dipterum as a new model system to investigate insect evolution. Evodevo 10, 6.

 

Almudi, I., McGregor, A.P., 2019. Sensory Organ Size Evolution: A View from Drosophila. Developmental Cell 50, 673-674.

 

Gaspar, P.*, Almudi, I.*, Nunes, M.D.S., McGregor, A.P., 2019. Human eye conditions: insights from the fly eye. Human Genetics 138, 973-991.

 

Torres-Mendez, A., Bonnal, S., Marquez, Y., Roth, J., Iglesias, M., Permanyer, J., Almudi, I., O'Hanlon, D., Guitart, T., Soller, M., Gingras, A.C., Gebauer, F., Rentzsch, F., Blencowe, B.J., Valcarcel, J., Irimia, M., 2019. A novel protein domain in an ancestral splicing factor drove the evolution of neural microexons. Nature Ecology & Evolution 3, 691-701.

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Almudi, I*#. and J. Pascual-Anaya*# (2019). How Do Morphological Novelties Evolve? Novel Approaches to Define Novel Morphologies. Old Questions and Young Approaches to Animal Evolution. J. M. Martín-Durán & B. C. Vellutini. Cham, Springer International Publishing: 107-132.

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2018

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Kittelmann, S., Buffry, A.D., Franke, F.A., Almudi, I., Yoth, M., Sabaris, G., Couso, J.P., Nunes, M.D.S., Frankel, N., Gomez-Skarmeta, J.L., Pueyo-Marques, J., Arif, S., McGregor, A.P., 2018. Gene regulatory network architecture in different developmental contexts influences the genetic basis of morphological evolution. PLoS Genetics 14, e1007375.

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2016

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Casares, F., Almudi, I., 2016. Fast and Furious 800. The Retinal Determination Gene Network in Drosophila, in: Castelli-Gair Hombría, J., Bovolenta, P. (Eds.), Organogenetic Gene Networks: Genetic Control of Organ Formation. Springer International Publishing, Cham, pp. 95-124.

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Torres-Oliva, M., Almudi, I., McGregor, A.P., Posnien, N., 2016. A robust (re-)annotation approach to generate unbiased mapping references for RNA-seq-based analyses of differential expression across closely related species. BMC Genomics 17, 392.

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Dissmeyer N. Faden F, Ramezani T, Mielke S, Almudi I, Nairz K, Froehlich MS, Höckendorff J, Brandt W, Hoehenwarter W, Dohmen RJ, Schnittger A.. Phenotypes on demand via switchable target protein degradation in multicellular organisms. Nature Communications. 7, 12202.

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2014

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Hilbrant, M., Almudi, I., Leite, D.J., Kuncheria, L., Posnien, N., Nunes, M.D., McGregor, A.P., 2014. Sexual dimorphism and natural variation within and among species in the Drosophila retinal mosaic. BMC Evolutionary Biology 14, 240.

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2013

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Arif, S.*, Hilbrant, M.*, Hopfen, C.*, Almudi, I., Nunes, M.D., Posnien, N., Kuncheria, L., Tanaka, K., Mitteroecker, P., Schlotterer, C., McGregor, A.P., 2013. Genetic and developmental analysis of differences in eye and face morphology between Drosophila simulans and Drosophila mauritiana. Evolution & Development 15, 257-267.

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Arif, S.*, Murat, S.*, Almudi, I., Nunes, M.D., Bortolamiol-Becet, D., McGregor, N.S., Currie, J.M., Hughes, H., Ronshaugen, M., Sucena, E., Lai, E.C., Schlotterer, C., McGregor, A.P., 2013. Evolution of mir-92a underlies natural morphological variation in Drosophila melanogaster. Current Biology 23, 523-528.

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Almudi I., Poernbacher, Hafen and Stocker H., 2013. The Lnk/SH2B adaptor provides a fail-safe mechanism to establish the Insulin receptor-Chico interaction. Cell Communication & Signaling 11, 26.

Mora N., Almudi I., Alsina B., Corominas M. and Serras F., 2013. Beta amyloid protein precursor-like is a Ras1/MAPK-regulated gene required for axonal targeting in Drosophila photoreceptor neurons. Journal of Cell Science 126, 53-59.

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2010

Almudi I, Corominas M, Serras F, 2010. Competition between SOCS36E and Drk modulates Sevenless receptor tyrosine kinase activity. Journal of Cell Science, 123(Pt 22):3857-3862.

 

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2009
Almudi I, Stocker H, Hafen E, Corominas M, Serras F, 2009. SOCS36E specifically interferes with Sevenless signaling during Drosophila eye development. Developmental Biology 326(1):212-223.

 

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