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The full list of Publications from Cosma group can be found at:




  • Garate X, Gómez-García PA, Fernández Merino M, Cadevall Angles M, Zhu C, Castells-García A, Ed-daoui AI, Martin L, Ochiai H, Neguembor MV, Cosma MP (2024). The relationship between nanoscale genome organization and gene expression in mouse embryonic stem cells during pluripotency transition. Nucleic Acids Research June 8
  • Martinez-Sarmiento, J.A., Cosma, MP # and Lakadamyali, M. # (2024). Dissecting gene activation and chromatin remodeling dynamics in single human cells undergoing reprogramming. Cell Reports, May 2;43(5):114170
  • Nakagawa S, Carnevali D, Xiangtian T, Alvarez MJ, Parfitt D-E, Di Vicino U, Arumugam K, Shin W, Aranda S, Normanno D, Sebastian-Perez R, Cannatá C, Cortes P, Neguembor MV, Shen MM, Califano A#, Cosma MP# (2024). The Wnt-dependent master regulator NKX1-2 controls mouse pre-implantation development. Stem Cell Reports, Apr 26:S2213-6711(24)00110-3.





  • Martin, L.; Neguembor, M.V.#; Cosma, M.P. # (2023). Women’s contribution in understanding how topoisomerases and supercoiling control genome organization Frontiers in Molecular Bioscience, 27 March
  • Cosma, M.P. #; Neguembor, M.V.# (2023). The magic of unraveling genome architecture and function. Cell Reports, Apr 8;:112361# corresponding author
  • Martin, L.; Castells-García, A.; Cosma M.P.#; Neguembor, M.V.# (2023) STORM microscopy and cluster analysis for PcG studies. Book: Polycomb Group Proteins – Methods and Protocols, Springer ISBN 978-1-4939-6380-5, in press in second edition. #corresponding author




  • Neguembor MV, Arcon JP, Buitrago D, Lema R, Walther J, Garate X, Martin L, Romero P, AlHaj Abed J, Gut M, Blanc J, Lakadamyali M, Wu CT, Brun Heath I, Orozco M, Dans PD, Cosma MP (2022). MiOS, an integrated imaging and computational strategy to model gene folding with nucleosome resolution. Nature Structural & Molecular Biology 2022 October 11 ;29(10):1011-1023
  • Sergi Àngel Bonilla-Pons, Shoma Nakagawa, Elena Garreta Bahima, Álvaro Fernández-Blanco, Martina Pesaresi, Justin Christopher D’Antin, Ruben Sebastian-Perez, Daniela Greco, Eduardo Domínguez-Sala, Raúl Gómez-Riera, Rafael Ignacio Barraquer Compte, Mara Dierssen, Nuria Montserrat Pulido, Maria Pia Cosma (2022). Müller glia fused with adult stem cells undergo neural differentiation in human retinal models. EBioMedicine 2022 Mar 9;77:103914
  • Alvaro Castells-Garcia, Ilyas Ed-daoui, Esther González-Almela, Chiara Vicario, Jason Ottestrom, Melike Lakadamyali, Maria Victoria Neguembor, Maria Pia Cosma (2022). Super resolution microscopy reveals how elongating RNA polymerase II and nascent RNA interact with nucleosome clutches. Nucleic Acids Research, 2022 Jan 11;50(1):175-190





  • Neguembor, MV, Martin L, Castells-García A, Gómez-García, PA, Vicario, C, Carnevali, D, AlHaj Abed, J, Granados, A, Sebastian-Perez, R, Sottile, F, Solon, J, Wu, CT, Lakadamyali, L, and Cosma MP (2021). Transcription-mediated supercoling regulates genome folding and loop formation. Molecular Cell, Aug 5;81(15):3065-3081.e12. Epub 2021 Jul 22.
  • Gomez‐Garcia PA, Portillo‐Ledesma S, Neguembor MV, Pesaresi M, Oweis W, Rohrlich T, Wieser S, Meshorer E, Schlick T, *Cosma MP, and *Lakadamyali (2021). M. Mesoscale modeling and single nucleosome tracking reveal remodeling of clutch folding and dynamics in stem cell differentiation. Cell Reports Jan 12th *co-last authors
  • Pesaresi M, Bonilla SA, Sebastian R, Di Vicino U, Alcoverro M, Michael R, Cosma MP (2021). The Chemokine Receptors Ccr5 and Cxcr6 Enhance Migration of Mesenchymal Stem Cells into the Degenerating Retina. Molecular Therapy 2021 29(2):804-821




  • Arumugam K, Shin W, Schiavone V, Vlahos L, Tu X, Carnevali D, Kesner J, Paull EO, Romo N, Subramaniam P, Worley J, Tan X, Califano A, Cosma MP (2020). The Master Regulator Protein BAZ2B Can Reprogram Human Hematopoietic Lineage-Committed Progenitors into a Multipotent State. Cell Reports  33(10):108474
  • Aulicino F, Pedone E, Sottile F, Lluis F, Marucci L, Cosma MP (2020). Canonical Wnt Pathway Controls mESC Self-Renewal Through Inhibition of Spontaneous Differentiation via β-Catenin/TCF/LEF Functions. Stem Cell Reports 2020 3:646-661
  • Lakadamyali M, Cosma MP (2020). Visualizing the genome in high resolution challenges our textbook understanding. Nature Methods 17:371–379





  • Frade J, Nakagawa S, Cortes P, di Vicino U, Romo N, Lluis F, Cosma MP. Controlled ploidy reduction of pluripotent 4n cells generates 2n cells during mouse embryo development. Sci Adv. 2019 Oct 16th..
  • Otterstrom J, Castells-Garcia A, Vicario C, Gomez-Garcia PA, Cosma MP, Lakadamyali M. Super-resolution microscopy reveals how histone tail acetylation affects DNA compaction within nucleosomes in vivo. Nucleic Acids Res. 2019 Sep 19th
  • Theka I, Sottile F, Cammisa M, Bonnin S, Sanchez-Delgado M, Di Vicino U, Neguembor MV, Arumugam K, Aulicino F, Monk D, Riccio A, Cosma MP. Wnt/β-catenin signaling pathway safeguards epigenetic stability and homeostasis of mouse embryonic stem cells. Sci Rep. 2019 Jan 30th





  • Pesaresi M, Bonilla-Pons SA, Simonte G, Sanges D, Di Vicino U, Cosma MP. Endogenous Mobilization of Bone-Marrow Cells Into the Murine Retina Induces Fusion-Mediated Reprogramming of Müller Glia Cells. EBioMedicine. 2018 Apr
  • Neguembor MV, Sebastian-Perez R, Aulicino F, Gomez-Garcia PA, *Cosma MP, *Lakadamyali M (2018). (Po)STAC (Polycistronic SunTAg modified CRISPR) enables live-cell and fixed-cell super-resolution imaging of multiple genes. Nucleic Acids Research; *co-last authors




  • Theka I, Sottile F, Aulicino F, Castells Garcia A  and Cosma MP (2017). Reduced expression of Paternally Expressed Gene-3 enhances somatic cell reprogramming through mitochondrial activity perturbation, Scientific Reports. Aug 29;7(1):9705.
  • De Jaime-Soguero A, Aulicino F, Ertaylan G,  Grieco A, Cerrato A, Tallam A, del Sol A,  *Cosma MP and *Lluis F and (2017). Wnt/b-catenin/Tcf1 pathway controls mouse embryonic stem cell cycle progression and proliferation by regulating the Ink4/Arf locus. Plos Genetics *co-last authors 27;13(3).
  • Pedone E, Olteanu VA, Marucci L, Muñoz-Martin MI, Youssef SA, de Bruin A, Cosma MP (2017).Modeling Dynamics and Function of Bone Marrow Cells in Mouse Liver Regeneration. Cell Reports. 2017 Jan 3;18(1):107-121





  • Sottile F, Aulicino F, Theka I, Cosma MP (2016). Mesenchymal stem cells generate distinct functional hybrids in vitro via cell fusion or entosis. Scientific Reports, 2016 Nov 9;6:36863
  • Sanges D, Simonte G, Di Vicino U, Romo N, Pinilla I, Nicolás M, and Cosma MP (2016). Reprogramming Müller glia via in vivo cell fusion regenerates murine photoreceptors. Journal Clinical Investigation, Aug 1;126(8):3104-3116
  • Altarche-Xifro W, di Vicino U, Muñoz-Martin MI, Bové J, Vila M and Cosma MP (2016). Functional rescue of dopaminergic neuron loss in Parkinson’s disease mice after transplantation of hematopoietic stem and progenitor cells. EBioMedicine, Jun;8:83-95





  • Ricci MA, Manzo C, García-Parajo M, *Lakadamyali M, and *Cosma MP (2015). Chromatin fibers are formed by heterogeneous groups of nucleosomes in vivo. Cell, *co-last authors. Nominated F1000Prime 2015





  • Marucci L, Pedone E, Di Vicino U, Isalan M, Cosma MP (2014). beta-catenin and Nanog fluctuate synchronously in mouse ESCs and cooperate to enhance reprogramming of somatic cells to pluripotency. Cell Reports, Sep 25;8(6):1686-96.
  • Aulicino F, Theka I, Ombrato L, Lluis F, Cosma MP (2014) Temporal perturbation of the Wnt signalling pathway controls cell reprogramming via Tcf1 activity. Stem Cell Reports, May 8;2(5):707-20.





  • Sanges D, Romo N, Simonte G, Di Vicino U, Tahoces AD, Fernández E, Cosma MP. (2013) Wnt/β-Catenin Signaling Triggers Neuron Reprogramming and Regeneration in the Mouse Retina. Cell Reports Jul 25;4(2):271-86.





  • Lluis F, Ombrato L, Pedone E, Pepe S, Merrill BJ, Cosma MP. (2011) T-cell factor 3 (Tcf3) deletion increases somatic cell reprogramming by inducing epigenome modifications. PNAS Jul 19;108(29):11912-7





  • Cantone I, Marucci L, Iorio F, Ricci MA, Belcastro V, Bansal M, di Bernardo M, Santini D, *di Bernardo D and *Cosma MP (2009). A yeast synthetic network for In-vivo assessment of reverse-engineering and modelling approaches. Cell Apr 3;137(1):172-81. *co-last authors





  • Lluis F, Pedone E, Pepe S, Cosma MP (2008). Periodic activation of Wnt/beta-catenin signalling enhances somatic cell reprogramming mediated by cell fusion. Cell Stem Cell. Nov 6;3(5):493-507