PUBLICATIONS
 \  PUBLICATIONS

2021

 

López-Delgado AC, Delgado I, Cadenas V, Sánchez-Cabo F, and Torres M (2021). Axial skeleton anterior-posterior patterning is regulated through feedback regulation between Meis transcription

factors and retinoic acid. Development, 148: dev193813. doi: 10.1242/dev.193813

 

Delgado I, Giovinazzo G, Temiño S, Gauthier Y, Balsalobre A, Drouin J and Torres M (2021). Control of mouse limb initiation and antero-posterior patterning by Meis transcription factors. Nature Communications, 12:3086. doi: 10.1038/s41467-021-23373-9

 

Zhu R, Rio-Salgado JM del, Garcia-Ojalvo J, Elowitz MB. Synthetic multistability in mammalian cells. bioRxiv 2021; 2021.02.10.430659. https://doi.org/10.1101/2021.02.10.430659

 

Torregrosa G, Garcia-Ojalvo J. Mechanistic models of cell-fate transitions from single-cell data. Current Opinion in Systems Biology 2021; 26: 79-86. https://doi.org/10.1016/j.coisb.2021.04.004

 

Bastounis EE, Serrano-Alcalde F, Radhakrishnan P, Engström P, Gómez-Benito MJ, Oswald MS, Yeh YT, Smith JG, Welch MD, García-Aznar JM, Theriot JA. Mechanical competition triggered by innate immune signaling drives the collective extrusion of bacterially infected epithelial cells. Dev Cell. 2021; 56(4):443-460.e11, https://doi.org/10.1016/j.devcel.2021.01.012.

 

Hervas-Raluy S, Gomez-Benito MJ, Borau-Zamora C, Cóndor M, Garcia-Aznar JM. A new 3D finite element-based approach for computing cell surface tractions assuming nonlinear conditions. PLoS One. 2021; 16(4):e0249018, https://doi.org/10.1371/journal.pone.0249018.

 

García-Aznar JM, Nasello G, Hervas-Raluy S, Pérez MÁ, Gómez-Benito MJ. Multiscale modeling of bone tissue Mechanobiology. Bone. 2021:116032, https://doi.org/10.1016/j.bone.2021.116032.

 

Gonçalves IG, Garcia-Aznar JM. Extracellular matrix density regulates the formation of tumour spheroids through cell migration. PLoS Comput Biol. 2021; 17(2):e1008764, https://doi.org/10.1371/journal.pcbi.1008764.

 

Betegón-Putze I, Mercadal J, Bosch N, Planas-Riverola A, Marquès-Bueno M, Vilarrasa-Blasi J, Frigola D, Burkart RC, Martínez C, Conesa A, Sozzani R, Stahl Y, Prat S, Ibañes M, Caño-Delgado AI. “Precise transcriptional control of cellular quiescence by BRAVO/WOX5 complex in Arabidopsis roots.” Mol Syst Biol. 17(6):e9864 (2021).

 

Pradillo, J.M., Hernández-Jiménez, M., Fernández-Valle, M.E., Medina, V., Ortuño, J.E., Allan, S.M., Proctor, S.D., Garcia-Segura, J.M., Ledesma-Carbayo, M.J., Santos, A., Moro, M.A., Lizasoain, I. “Influence of metabolic syndrome on post-stroke outcome, angiogenesis and vascular function in old rats determined by dynamic contrast enhanced MRI”. J. Cereb. Blood Flow Metab., 41(7):1692-1706. 2021 (doi: 10.1177/0271678X20976412).

 

2020

 

Fernandez-Guerrero M, Yakushiji-Kaminatsui N, Lopez-Delisle L, Zdral S, Darbellay F, Perez-Gomez R, et al. Mammalian-specific ectodermal enhancers control the expression of Hoxc genes in developing nails and hair follicles. Proc Natl Acad Sci. 2020; 117(48):30509–19, https://doi.org/10.1073/pnas.2011078117.

 

Busby L, Aceituno C, McQueen C, Rich CA, Ros MA*, Towers M.* Sonic hedgehog specifies flight feather positional information in avian wings. Dev. 2020; 147(9):dev188821, https://doi.org/10.1242/DEV.188821.

 

Bastida MF, Pérez-Gómez R, Trofka A, Zhu J, Rada-Iglesias A, Sheth R, et al. The formation of the thumb requires direct modulation of Gli3 transcription by Hoxa13. Proc Natl Acad Sci. 2020; 117(2):1090–1096, https://doi.org/10.1073/pnas.1919470117.

 

Lioux G, Liu, X, Temiño S, Oxendine M, Ayala E, Ortega S, Kelly RG, Oliver G and Torres M (2020). A Second Heart Field-derived vasculogenic niche contributes to cardiac lymphatics. Developmental Cell, 52:350-363. doi: 10.1016/j.devcel.2019.12.006

 

Delgado I, López-Delgado AC, Roselló-Díez A, Giovinazzo G, Cadenas V, Fernández-de-Manuel L, Sánchez-Cabo F, Anderson MJ, Lewandoski M and Torres M (2020). Proximo-distal positional information encoded by an Fgf-regulated gradient of homeodomain transcription factors in the vertebrate limb. Science Advances, 6(23), EAAZ0742

 

Cotterell J, Vila-Cejudo M, Batlle-Morera L, Sharpe J. (2020) Endogenous CRISPR/Cas9 arrays for scalable whole-organism lineage tracing. Development 147(9). DOI: 10.1242/dev.184481.

 

Saiz N, Mora-Bitria L, Rahman S, George H, Herder J, Garcia-Ojalvo J, et al. Growth factor-mediated coupling between lineage size and cell fate choice underlies robustness of mammalian development. eLife 2020; 9: e56079. https://doi.org/10.7554/eLife.56079

 

Matsuda M, Hayashi H, Garcia-Ojalvo J, Yoshioka-Kobayashi K, Kageyama R, Yamanaka Y, et al. Species-specific segmentation clock periods are due to differential biochemical reaction speeds. Science 2020; 369(6510): 1450–5. https://doi.org/10.1126/science.aba7668

 

Galera-Laporta L, Garcia-Ojalvo J. Antithetic population response to antibiotics in a polybacterial community. Science Advances 2020; 6(10): eaaz5108. https://doi.org/10.1126/sciadv.aaz5108

 

Barrio L., and Milán M “Regulation of anisotropic tissue growth by two orthogonal signaling centers” Developmental Cell, 52(5):659-672 (2020)

 

Almudi I, Vizueta J, Wyatt CDR, de Mendoza A, Marlétaz F, Firbas PN, Feuda R, Masiero G, Medina P, Alcaina-Caro A, Cruz F, Gómez-Garrido J, Gut M, Alioto TS, Vargas-Chavez C, Davie K, Misof B, González J, Aerts S, Lister R, Paps J, Rozas J, Sánchez-Gracia A, Irimia M, Maeso I, Casares F. Genomic adaptations to aquatic and aerial life in mayflies and the origin of insect wings. Nat Commun. 2020 May 26;11(1):2631. doi: 10.1038/s41467-020-16284-8.

 

Casares F, McGregor AP. The evolution and development of eye size in flies. Wiley Interdiscip Rev Dev Biol. 2020 May 12:e380. doi: 10.1002/wdev.380.

 

Míguez DG, García-Morales D, Casares F. Control of size, fate and time by the Hh morphogen in the eyes of flies. Curr Top Dev Biol. 2020;137:307-332. doi: 10.1016/bs.ctdb.2019.10.011.

 

Ruiz-Sobrino A, Martín-Blanco CA, Navarro T, Almudí I, Masiero G, Jiménez-Caballero M, Buchwalter DB, Funk DH, Gattolliat JL, Lemos MC, Jiménez F, Casares F. Space colonization by branching trachea explains the morphospace of a simple respiratory organ. Dev Biol. 2020 Jun 1;462(1):50-59. doi: 10.1016/j.ydbio.2020.02.005.

 

Nieto A, Escribano J, Spill, F, Garcia-Aznar, JM, Gomez-Benito, MJ. Finite element simulation of the structural integrity of endothelial cell monolayers: A step for tumor cell extravasation, Engineering Fracture Mechanics, 2020; 224, https://doi.org/10.1016/j.engfracmech.2019.106718.

 

Sancho JM, Ibañes M.” Landau theory for cellular patterns driven by lateral inhibition interaction. “Phys Rev E. 102(3-1):032404 (2020).

The transition from local to global patterns governs the differentiation of mouse blastocysts.  Fischer SC, Corujo-Simon E, Lilao-Garzon J, Stelzer EHK, Muñoz-Descalzo S. PLoS One. 2020;15(5):e0233030. doi:10.1371/journal.pone.0233030

 

Ortuño, J.E., Vegas-Sánchez-Ferrero, G., Gómez-Valverde, J.J., Chen, M.Y., Santos, A., McVeigh, E.R., Ledesma-Carbayo, M.J. “Automatic estimation of aortic and mitral valve displacements in dynamic CTA with 4D graph-cuts”. Med. Image Anal., 65:101748. 2020 (doi: 10.1016/j.media.2020.101748).

 

Bermejo-Peláez, D., Ash, S.Y., Washko, G.R., San José Estépar, R., Ledesma-Carbayo, M.J. “Classification of Interstitial Lung Abnormality Patterns with an Ensemble of Deep Convolutional Neural Networks”. Sci Rep, 10:338. 2020 (doi: 10.1038/s41598-019-56989-5).

 

2019

 

Lioux G, Liu, X, Temiño S, Oxendine M, Ayala E, Ortega S, Kelly RG, Oliver G and Torres M (2020). A Second Heart Field-derived vasculogenic niche contributes to cardiac lymphatics. Developmental Cell, 52:350-363. doi: 10.1016/j.devcel.2019.12.006

 

Sharpe J. (2019) Wolpert’s French Flag: what’s the problem? Development 146(24). DOI: 10.1242/dev.185967.

 

Germann P, Marin-Riera M, Sharpe J. (2019) ya||a: GPU-Powered Spheroid Models for Mesenchyme and Epithelium. Cell Systems 8(3):261-266.e3. DOI: 10.1016/j.cels.2019.02.007.

 

Martinez-Corral Rosa, Liu Jintao, Prindle Arthur, Süel Gürol M., Garcia-Ojalvo Jordi. Metabolic basis of brain-like electrical signalling in bacterial communities. Philosophical Transactions of the Royal Society B 2019; 374(1774): 20180382. https://doi.org/10.1098/rstb.2018.0382

 

Míguez DG, García-Morales D, Casares F. Control of size, fate and time by the Hh morphogen in the eyes of flies. Curr Top Dev Biol. 2020;137:307-332. doi: 10.1016/bs.ctdb.2019.10.011.

 

A toggle-switch and a feed-forward loop engage in the control of the Drosophila retinal determination gene network. M Sánchez-Aragón #, J. Cantisán#, C.S. Lopes, C.M Luque, M.C. Lemos*, F. Casares* (2019). Frontiers in Ecology and Evolution, section Evolutionary Developmental Biology. doi.org/10.3389/fevo.2019.00221.

 

Dynamic Hh signaling can generate temporal information during tissue patterning. D Garcia-Morales, T Navarro, A. Iannini, DG Miguez*, Fernando Casares*. 2019. Development Apr 25;146(8). doi: 10.1242/dev.176933. doi.org/10.1101/451872

 

Mouse ICM Organoids Reveal Three-Dimensional Cell Fate Clustering. Mathew B, Muñoz-Descalzo S, Corujo-Simon E, Schröter C, Stelzer EHK, Fischer SC. Biophys J. 2019;116(1):127‐141. doi:10.1016/j.bpj.2018.11.011

 

Nieto A, Escribano J, Spill, F, Garcia-Aznar, JM, Gomez-Benito, MJ. Finite element simulation of the structural integrity of endothelial cell monolayers: A step for tumor cell extravasation, Engineering Fracture Mechanics, 2020; 224, https://doi.org/10.1016/j.engfracmech.2019.106718.

 

Planas-Riverola A, Gupta A, Betegón-Putze I, Bosch N, Ibañes M, Caño-Delgado AI. “Brassinosteroid signaling in plant development and adaptation to stress “Development 146(5):dev151894. (2019) Review.

 

Pablo-Trinidad, A., Butterworth, I., Ledesma-Carbayo, M.J., Vettenburg, T., Sánchez-Ferro, A., Soenksen, L., Durr, N.J., Muñoz-Barrutia, A., Cerrato, C., Humala, K., Fabra Urdiol, M., Del Rio, C., Valles, B., Chen, Y.-B., Hochberg, E.P., Castro-González, C., Bourquard, A. “Automated detection of neutropenia using noninvasive video microscopy of superficial capillaries”. Am. J. Hematol., 94(8):E219-E222. 2019 (doi: 10.1002/ajh.25516).

 

Gkontra, P., El-Bouri, W.K., Norton, K.-A., Santos, A., Popel, A.S., Payne, S.J., Arroyo, A.G. “Dynamic Changes in Microvascular Flow Conductivity and Perfusion after Myocardial Infarction Shown by Image-Based Modeling”. J. Am. Heart Assoc., 8:e011058. 2019 (doi: 10.1161/JAHA.118.011058).

 

Gómez-Valverde, J.J., Antón, A., Fatti, G., Liefers, B., Herranz, A., Santos, A., Sánchez, C.I., Ledesma-Carbayo, M.J. “Automatic glaucoma classification using color fundus images based on convolutional neural networks and transfer learning”. Biomed. Opt. Express, 10(2):892-913. 2019 (doi: 10.1364/BOE.10.000892).

 

Linares, M., Postigo, M., Cuadrado, D., Ortiz-Ruiz, A., Gil-Casanova, S., Vladimirov, A., García-Villena, J., Nuñez-Escobedo, J.M., Martínez-López, J., Rubio, J.M., Ledesma-Carbayo, M.J., Santos, A., Bassat, Q., Luengo-Oroz, M. “Collaborative Intelligence and Gamification for On-Line Malaria Species Differentiation”. Malar. J., 18:21. 2019 (doi: 10.1186/s12936-019-2662-9).

 

2018

 

Pérez-gómez R, Haro E, Fernández-guerrero M, Bastida MF, Ros MA. Role of Hox genes in regulating digit patterning. Int J Dev Biol. 2018; 805:797–805, https://doi.org/10.1387/IJDB.180200MR.

 

Pickering J, Rich CA, Stainton H, Aceituno C, Chinnaiya K, Saiz-Lopez P, et al. An intrinsic cell cycle timer terminates limb bud outgrowth. Elife. 2018; 7:e37429, https://doi.org/10.7554/eLife.37429.

 

Diego X, Marcon L, Muller P, Sharpe J. (2018). Key Features of Turing Systems are Determined Purely by Network Topology. PHYSICAL REVIEW X. doi:10.1103/PhysRevX.8.021071.

 

Martinez-Corral Rosa, Liu Jintao, Prindle Arthur, Süel Gürol M., Garcia-Ojalvo Jordi. Metabolic basis of brain-like electrical signalling in bacterial communities. Philosophical Transactions of the Royal Society B 2019; 374(1774): 20180382. https://doi.org/10.1098/rstb.2018.0382

 

Martinez-Corral R, Raimundez E, Lin Y, Elowitz MB, Garcia-Ojalvo J. Self-Amplifying Pulsatile Protein Dynamics without Positive Feedback. Cell Systems 2018; 7(4): 453-462.e1. https://doi.org/10.1016/j.cels.2018.08.012

 

Benhra N., Barrio L., Muzzopappa M. and Milán M “Chromosomal instability induces cellular invasion in epithelial tissues” Developmental Cell, 47(2):161-174 (2018)

 

Mouse ICM Organoids Reveal Three-Dimensional Cell Fate Clustering. Mathew B, Muñoz-Descalzo S, Corujo-Simon E, Schröter C, Stelzer EHK, Fischer SC. Biophys J. 2019;116(1):127‐141. doi:10.1016/j.bpj.2018.11.011

 

Merino-Casallo F, Gomez-Benito MJ, Juste-Lanas Y, Martinez-Cantin R, Garcia-Aznar JM. Integration of in vitro and in silico Models Using Bayesian Optimization With an Application to Stochastic Modeling of Mesenchymal 3D Cell Migration. Front Physiol. 2018; 11; 9:1246, https://doi.org/10.3389/fphys.2018.01246.

 

Pavelescu I, Vilarrasa-Blasi J, Planas-Riverola A, González-García MP, Caño-Delgado AI, Ibañes M. “A Sizer model for cell differentiation in Arabidopsis thaliana root growth“ Mol Syst Biol. 14(1):e7687 (2018).

 

Luna-Escalante JC, Formosa-Jordan P, Ibañes M. “Redundancy and cooperation in Notch intercellular signaling” Development 145(1):dev154807 (2018).

 

Gkontra, P., Norton, K.-A., Żak, M.M., Clemente, C., Agüero, J., Ibáñez, B., Santos, A., Popel, A.S., Arroyo, A.G. “Deciphering microvascular changes after myocardial infarction through 3D fully automated image analysis”. Sci Rep, 8:1854. 2018 (doi: 10.1038/s41598-018-19758-4).

 

2017

 

Saiz-Lopez P, Chinnaiya K, Towers M, Ros MA. Intrinsic properties of limb bud cells can be differentially reset. Development. 2017; 144(3):479–86, https://doi.org/10.1242/dev.137661.

 

Recasens-Alvarez C., Ferreira A. and Milán M. “JAK/STAT controls organ size and fate specification by regulating morphogen production and Signaling” Nature Communications, 8:13815 (2017)

 

Barrio L., and Milán M “Boundary Dpp promotes growth of medial and lateral regions of the Drosophila wing” eLife. DOI: 10.7554/eLife.22013 (2017)

 

Muzzopappa M, Murcia L, and Milán M. “Feedback amplification loop drives malignant growth in epithelial tissues” Proc Natl Acad Sci U S A. 114(35): E7291-E7300 (2017)

 

Growth and Size Control during Development. Vollmer J, Casares F*, Iber D*. Open Biol. 2017 Nov;7(11). pii: 170190. doi: 10.1098/rsob.170190. Review

 

2016

 

Onimaru K, Marcon L, Musy M, Tanaka M, Sharpe J. (2016) The fin-to-limb transition as the re-organization of a Turing pattern. Nature Communications 7:11582. DOI: 10.1038/ncomms11582.

 

Clemente-Ruiz M., Murillo-Maldonado J.M., Benhra N., Barrio L., Pérez L., Quiroga G., Nebreda A.R., Milán M. “Gene dosage imbalance contributes to chromosomal instability-induced tumorigenesis” Developmental Cell, 36(3):290-302 (2016)

 

2015

 

Uzkudun M, Marcon L, Sharpe J. (2015) Data-driven modelling of a gene regulatory network for cell fate decisions in the growing limb bud. Molecular Systems Biology. 11(7):815. DOI: 10.15252/msb.20145882.

 

Ferreira A., and Milán M. “Dally proteoglycan mediates the autonomous and non-autonomous effects on tissue growth caused by activation of the PI3K and TOR pathways”. PloS Biology 13(8):e1002239 (2015)

 

Wnt/β-catenin signalling and the dynamics of fate decisions in early mouse embryos and embryonic stem (ES) cells.  Muñoz-Descalzo S, Hadjantonakis AK, Arias AM. Semin Cell Dev Biol. 2015;47-48:101‐109. doi:10.1016/j.semcdb.2015.08.011

 

2014

 

Uzkudun M, Marcon L, Sharpe J. (2015) Data-driven modelling of a gene regulatory network for cell fate decisions in the growing limb bud. Molecular Systems Biology. 11(7):815. DOI: 10.15252/msb.20145882.

 

Raspopovic J, Marcon L, Russo L, Sharpe J. (2014) Digit patterning is controlled by a Bmp-Sox9-Wnt Turing network modulated by morphogen gradients. Science 345(6196):566-570. DOI: 10.1126/science.1252960.

 

Oct4 is required for lineage priming in the developing inner cell mass of the mouse blastocyst.  Le Bin, G. C., Muñoz-Descalzo, S., Kurowski, A., Leitch, H., Lou, X., Mansfield, W., Etienne-Dumeau, C., Grabole, N., Mulas, C., Niwa, H., Hadjantonakis, A. K., & Nichols, J. Development. 2014;141(5):1001‐1010. doi:10.1242/dev.096875

 

2013

 

Barrio L., and Milán M “Boundary Dpp promotes growth of medial and lateral regions of the Drosophila wing” eLife. DOI: 10.7554/eLife.22013 (2017)

 

A membrane-associated β-catenin/Oct4 complex correlates with ground-state pluripotency in mouse embryonic stem cells. Faunes F; Hayward P; Descalzo SM; Chatterjee SS; Balayo T; Trott J; Christoforou A; Ferrer-Vaquer A; Hadjantonakis AK; Dasgupta R; Arias AM. Development 2013 140: 1171-1183; doi: 10.1242/dev.085654

 

A competitive protein interaction network buffers Oct4-mediated differentiation to promote pluripotency in embryonic stem cells. Muñoz Descalzo, S., Rué, P., Faunes, F., Hayward, P., Jakt, L. M., Balayo, T., Garcia-Ojalvo, J., & Martinez Arias, A.  Mol Syst Biol. 2013;9:694. Published 2013 Oct 8. doi:10.1038/msb.2013.49

 

2012

 

Correlations between the levels of Oct4 and Nanog as a signature for naïve pluripotency in mouse embryonic stem cells.  Muñoz Descalzo S, Rué P, Garcia-Ojalvo J, Martinez Arias A. Stem Cells. 2012;30(12):2683‐2691. doi:10.1002/stem.1230

 

2011

 

Fernandez-Guerrero M, Yakushiji-Kaminatsui N, Lopez-Delisle L, Zdral S, Darbellay F, Perez-Gomez R, et al. Mammalian-specific ectodermal enhancers control the expression of Hoxc genes in developing nails and hair follicles. Proc Natl Acad Sci. 2020; 117(48):30509–19, https://doi.org/10.1073/pnas.2011078117.