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2024 Journal Article Endothelial c-Src Mediates Neovascular Tuft Formation in Oxygen-Induced RetinopathyFrampton, Emmanuelle, Som, Priyanka, Hill, Brittany, Yu, Alexander, Naval-Sanchez, Marina, Nefzger, Chistian M., Noordstra, Ivar, Gordon, Emma and Schimmel, Lilian (2024). Endothelial c-Src Mediates Neovascular Tuft Formation in Oxygen-Induced Retinopathy. The American Journal of Pathology, 194 (12), 2239-2251. doi: 10.1016/j.ajpath.2024.09.003 |
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2024 Journal Article The activity of early-life gene regulatory elements is hijacked in aging through pervasive AP-1-linked chromatin openingPatrick, Ralph, Naval-Sanchez, Marina, Deshpande, Nikita, Huang, Yifei, Zhang, Jingyu, Chen, Xiaoli, Yang, Ying, Tiwari, Kanupriya, Esmaeili, Mohammadhossein, Tran, Minh, Mohamed, Amin R., Wang, Binxu, Xia, Di, Ma, Jun, Bayliss, Jacqueline, Wong, Kahlia, Hun, Michael L., Sun, Xuan, Cao, Benjamin, Cottle, Denny L., Catterall, Tara, Barzilai-Tutsch, Hila, Troskie, Robin-Lee, Chen, Zhian, Wise, Andrea F., Saini, Sheetal, Soe, Ye Mon, Kumari, Snehlata, Sweet, Matthew J. ... Nefzger, Christian M. (2024). The activity of early-life gene regulatory elements is hijacked in aging through pervasive AP-1-linked chromatin opening. Cell Metabolism, 36 (8), 1858-1881.e23. doi: 10.1016/j.cmet.2024.06.006 |
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2024 Journal Article Wnt dose escalation during the exit from pluripotency identifies tranilast as a regulator of cardiac mesodermWu, Zhixuan, Shen, Sophie, Mizikovsky, Dalia, Cao, Yuanzhao, Naval-Sanchez, Marina, Tan, Siew Zhuan, Alvarez, Yanina D., Sun, Yuliangzi, Chen, Xiaoli, Zhao, Qiongyi, Kim, Daniel, Yang, Pengyi, Hill, Timothy A., Jones, Alun, Fairlie, David P., Pébay, Alice, Hewitt, Alex W., Tam, Patrick P.L., White, Melanie D., Nefzger, Christian M. and Palpant, Nathan J. (2024). Wnt dose escalation during the exit from pluripotency identifies tranilast as a regulator of cardiac mesoderm. Developmental Cell, 59 (6), 705-722.e8. doi: 10.1016/j.devcel.2024.01.019 |
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2023 Journal Article Micrococcal nuclease sequencing of porcine sperm suggests enriched co-location between retained histones and genomic regions related to semen quality and early embryo developmentGòdia, Marta, Lian, Yu, Naval-Sanchez, Marina, Ponte, Inma, Rodríguez-Gil, Joan Enric, Sanchez, Armand and Clop, Alex (2023). Micrococcal nuclease sequencing of porcine sperm suggests enriched co-location between retained histones and genomic regions related to semen quality and early embryo development. PeerJ, 11 e15520, 1-25. doi: 10.7717/peerj.15520 |
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2022 Journal Article Leveraging transcriptome and epigenome landscapes to infer regulatory networks during the onset of sexual maturationMohamed, Amin R., Naval-Sanchez, Marina, Menzies, Moira, Evans, Bradley, King, Harry, Reverter, Antonio and Kijas, James W. (2022). Leveraging transcriptome and epigenome landscapes to infer regulatory networks during the onset of sexual maturation. BMC Genomics, 23 (1) 413, 1-19. doi: 10.1186/s12864-022-08514-8 |
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2022 Journal Article Organization of gene programs revealed by unsupervised analysis of diverse gene–trait associationsMizikovsky, Dalia, Naval Sanchez, Marina, Nefzger, Christian M, Cuellar Partida, Gabriel and Palpant, Nathan J (2022). Organization of gene programs revealed by unsupervised analysis of diverse gene–trait associations. Nucleic Acids Research, 50 (15) e87, 1-12. doi: 10.1093/nar/gkac413 |
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2022 Journal Article Benchmarking of ATAC Sequencing Data From BGI’s Low-Cost DNBSEQ-G400 Instrument for Identification of Open and Occupied Chromatin RegionsNaval-Sanchez, Marina, Deshpande, Nikita, Tran, Minh, Zhang, Jingyu, Alhomrani, Majid, Alsanie, Walaa, Nguyen, Quan and Nefzger, Christian M. (2022). Benchmarking of ATAC Sequencing Data From BGI’s Low-Cost DNBSEQ-G400 Instrument for Identification of Open and Occupied Chromatin Regions. Frontiers in Molecular Biosciences, 9 900323, 1-15. doi: 10.3389/fmolb.2022.900323 |
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2022 Journal Article Temporal perturbation of histone deacetylase activity reveals a requirement for HDAC1–3 in mesendoderm cell differentiationSinniah, Enakshi, Wu, Zhixuan, Shen, Sophie, Naval-Sanchez, Marina, Chen, Xiaoli, Lim, Junxian, Helfer, Abbigail, Iyer, Abishek, Tng, Jiahui, Lucke, Andrew J., Reid, Robert C., Redd, Meredith A., Nefzger, Christian M., Fairlie, David P. and Palpant, Nathan J. (2022). Temporal perturbation of histone deacetylase activity reveals a requirement for HDAC1–3 in mesendoderm cell differentiation. Cell Reports, 39 (7) 110818, 1-21. doi: 10.1016/j.celrep.2022.110818 |
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2021 Journal Article Chromatin accessibility and regulatory vocabulary across indicine cattle tissuesAlexandre, Pâmela A., Naval-Sánchez, Marina, Menzies, Moira, Nguyen, Loan T., Porto-Neto, Laercio R., Fortes, Marina R. S. and Reverter, Antonio (2021). Chromatin accessibility and regulatory vocabulary across indicine cattle tissues. Genome Biology, 22 (1) 273, 273. doi: 10.1186/s13059-021-02489-7 |
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2021 Journal Article A conserved haplotype in Wagyu cattle contains RAB4A whose encoded protein regulates glucose trafficking in muscle and fat cellsHudson, N. J., Porto-Neto, L., Naval-Sanchez, M., Lyons, R. E. and Reverter, Antonio (2021). A conserved haplotype in Wagyu cattle contains RAB4A whose encoded protein regulates glucose trafficking in muscle and fat cells. Animal Genetics, 52 (3), 275-283. doi: 10.1111/age.13054 |
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2021 Journal Article Analysis of polycerate mutants reveals the evolutionary co-option of HOXD1 for horn patterning in BovidaeAllais-Bonnet, Aurélie, Hintermann, Aurélie, Deloche, Marie-Christine, Cornette, Raphaël, Bardou, Philippe, Naval-Sanchez, Marina, Pinton, Alain, Haruda, Ashleigh, Grohs, Cécile, Zakany, Jozsef, Bigi, Daniele, Medugorac, Ivica, Putelat, Olivier, Greyvenstein, Ockert, Hadfield, Tracy, Jemaa, Slim Ben, Bunevski, Gjoko, Menzi, Fiona, Hirter, Nathalie, Paris, Julia M., Hedges, John, Palhiere, Isabelle, Rupp, Rachel, Lenstra, Johannes A., Gidney, Louisa, Lesur, Joséphine, Schafberg, Renate, Stache, Michael, Wandhammer, Marie-Dominique ... Capitan, Aurélien (2021). Analysis of polycerate mutants reveals the evolutionary co-option of HOXD1 for horn patterning in Bovidae. Molecular Biology and Evolution, 38 (6), 2260-2272. doi: 10.1093/molbev/msab021 |
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2021 Journal Article Nicotinamide riboside attenuates age-associated metabolic and functional changes in hematopoietic stem cellsSun, Xuan, Cao, Benjamin, Naval-Sanchez, Marina, Pham, Tony, Sun, Yu Bo Yang, Williams, Brenda, Heazlewood, Shen Y, Deshpande, Nikita, Li, Jinhua, Kraus, Felix, Rae, James, Nguyen, Quan, Yari, Hamed, Schröder, Jan, Heazlewood, Chad K, Fulton, Madeline, Hatwell-Humble, Jessica, Das Gupta, Kaustav, Kapetanovic, Ronan, Chen, Xiaoli, Sweet, Matthew J, Parton, Robert G, Ryan, Michael T, Polo, Jose M, Nefzger, Christian M and Nilsson, Susan K (2021). Nicotinamide riboside attenuates age-associated metabolic and functional changes in hematopoietic stem cells. Nature Communications, 12 (1) 2665, 1-17. doi: 10.1038/s41467-021-22863-0 |
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2020 Journal Article Genome-wide co-expression distributions as a metric to prioritize genes of functional importanceAlexandre, Pâmela A., Hudson, Nicholas J., Lehnert, Sigrid A., Fortes, Marina R. S., Naval-Sánchez, Marina, Nguyen, Loan T., Porto-Neto, Laercio R. and Reverter, Antonio (2020). Genome-wide co-expression distributions as a metric to prioritize genes of functional importance. Genes, 11 (10) 1231, 1231-13. doi: 10.3390/genes11101231 |
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2020 Journal Article Selection signatures in tropical cattle are enriched for promoter and coding regions and reveal missense mutations in the damage response gene HELBNaval-Sánchez, Marina, Porto-Neto, Laercio R., Cardoso, Diercles F., Hayes, Ben J., Daetwyler, Hans D., Kijas, James and Reverter, Antonio (2020). Selection signatures in tropical cattle are enriched for promoter and coding regions and reveal missense mutations in the damage response gene HELB. Genetics Selection Evolution, 52 (1) 27, 27. doi: 10.1186/s12711-020-00546-6 |
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2020 Journal Article Dynamics of gene co-expression networks in time-series data: a case study in Drosophila melanogaster embryogenesisLau, Li Yieng, Reverter, Antonio, Hudson, Nicholas J., Naval-Sanchez, Marina, Fortes, Marina R. S. and Alexandre, Pâmela A. (2020). Dynamics of gene co-expression networks in time-series data: a case study in Drosophila melanogaster embryogenesis. Frontiers in Genetics, 11 517, 517. doi: 10.3389/fgene.2020.00517 |
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2020 Journal Article Changed Patterns of Genomic Variation Following Recent Domestication: Selection Sweeps in Farmed Atlantic SalmonNaval-Sanchez, Marina, McWilliam, Sean, Evans, Bradley, Yáñez, José M., Houston, Ross D. and Kijas, James W. (2020). Changed Patterns of Genomic Variation Following Recent Domestication: Selection Sweeps in Farmed Atlantic Salmon. Frontiers in Genetics, 11 264. doi: 10.3389/fgene.2020.00264 |
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2020 Journal Article Association analysis of loci implied in 'buffering' epistasisReverter, Antonio, Vitezica, Zulma G., Naval-Sánchez, Marina, Henshall, John, Raidan, Fernanda, Li, Yutao, Meyer, Karin, Hudson, Nicholas J., Porto-Neto, Laercio R. and Legarra, Andrés (2020). Association analysis of loci implied in 'buffering' epistasis. Journal of Animal Science, 98 (3) skaa045. doi: 10.1093/jas/skaa045 |
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2019 Journal Article Systems biology reveals NR2F6 and TGFB1 as key regulators of feed efficiency in beef cattleAlexandre, Pâmela A., Naval-Sanchez, Marina, Porto-Neto, Laercio R., Ferraz, José Bento S., Reverter, Antonio and Fukumasu, Heidge (2019). Systems biology reveals NR2F6 and TGFB1 as key regulators of feed efficiency in beef cattle. Frontiers in Genetics, 10 (MAR) 230. doi: 10.3389/fgene.2019.00230 |
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2018 Journal Article Correction: Amniotic ectoderm expansion in mouse occurs via distinct modes and requires SMAD5-mediated signalling (vol 145, dev157222, 2018)Dobreva, Mariya P., Escalona, Vanesa Abon, Lawson, Kirstie A., Sanchez, Marina N., Ponomarev, Ljuba C., Pereira, Paulo N. G., Stryjewska, Agata, Criem, Nathan, Huylebroeck, Danny, Lopes, Susana M. Chuva de Sousa, Aerts, Stein and Zwijsen, An (2018). Correction: Amniotic ectoderm expansion in mouse occurs via distinct modes and requires SMAD5-mediated signalling (vol 145, dev157222, 2018). Development, 145 (15). doi: 10.1242/dev.169722 |
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2018 Journal Article Amniotic ectoderm expansion in mouse occurs via distinct modes and requires SMAD5-mediated signallingDobreva, Mariya P., Escalona, Vanesa Abon, Lawson, Kirstie A., Sanchez, Marina N., Ponomarev, Ljuba C., Pereira, Paulo N. G., Stryjewska, Agata, Criem, Nathan, Huylebroeck, Danny, Lopes, Susana M. Chuva de Sousa, Aerts, Stein and Zwijsen, An (2018). Amniotic ectoderm expansion in mouse occurs via distinct modes and requires SMAD5-mediated signalling. Development, 145 (13) dev157222, dev157222. doi: 10.1242/dev.157222 |
