The University of Queensland

Using cisTargetX to predict transcriptional targets and networks in Drosophila

Potier, Delphine, Atak, Zeynep Kalender, Sanchez, Marina Naval, Herrmann, Carl and Aerts, Stein (2012). Using cisTargetX to predict transcriptional targets and networks in Drosophila. Gene regulatory networks: methods and protocols. (pp. 291-314) edited by Bart Deplancke and Nele Gheldof. New York, NY, United States: Humana Press. doi: 10.1007/978-1-61779-292-2_18

The activity of early-life gene regulatory elements is hijacked in aging through pervasive AP-1-linked chromatin opening

Patrick, 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. doi: 10.1016/j.cmet.2024.06.006

Wnt dose escalation during the exit from pluripotency identifies tranilast as a regulator of cardiac mesoderm

Wu, 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

Micrococcal nuclease sequencing of porcine sperm suggests enriched co-location between retained histones and genomic regions related to semen quality and early embryo development

Gòdia, 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

Leveraging transcriptome and epigenome landscapes to infer regulatory networks during the onset of sexual maturation

Mohamed, 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

Organization of gene programs revealed by unsupervised analysis of diverse gene–trait associations

Mizikovsky, 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

Benchmarking of ATAC Sequencing Data From BGI’s Low-Cost DNBSEQ-G400 Instrument for Identification of Open and Occupied Chromatin Regions

Naval-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

Temporal perturbation of histone deacetylase activity reveals a requirement for HDAC1–3 in mesendoderm cell differentiation

Sinniah, 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

Chromatin accessibility and regulatory vocabulary across indicine cattle tissues

Alexandre, 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

A conserved haplotype in Wagyu cattle contains RAB4A whose encoded protein regulates glucose trafficking in muscle and fat cells

Hudson, 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

Analysis of polycerate mutants reveals the evolutionary co-option of HOXD1 for horn patterning in Bovidae

Allais-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

Nicotinamide riboside attenuates age-associated metabolic and functional changes in hematopoietic stem cells

Sun, 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

Genome-wide co-expression distributions as a metric to prioritize genes of functional importance

Alexandre, 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

Selection signatures in tropical cattle are enriched for promoter and coding regions and reveal missense mutations in the damage response gene HELB

Naval-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

Dynamics of gene co-expression networks in time-series data: a case study in Drosophila melanogaster embryogenesis

Lau, 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

Changed Patterns of Genomic Variation Following Recent Domestication: Selection Sweeps in Farmed Atlantic Salmon

Naval-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

Association analysis of loci implied in 'buffering' epistasis

Reverter, 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

Systems biology reveals NR2F6 and TGFB1 as key regulators of feed efficiency in beef cattle

Alexandre, 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

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

Amniotic ectoderm expansion in mouse occurs via distinct modes and requires SMAD5-mediated signalling

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). Amniotic ectoderm expansion in mouse occurs via distinct modes and requires SMAD5-mediated signalling. Development, 145 (13) dev157222, dev157222. doi: 10.1242/dev.157222

A haplotype information theory method reveals genes of evolutionary interest in European vs. Asian pigs

Hudson, Nicholas J., Naval-Sánchez, Marina, Porto-Neto, Laercio, Pérez-Enciso, Miguel and Reverter, Antonio (2018). A haplotype information theory method reveals genes of evolutionary interest in European vs. Asian pigs. Journal of Animal Science, 96 (8), 3064-3069. doi: 10.1093/jas/sky225

Evolution of sex determination loci in Atlantic salmon

Kijas, James, McWilliam, Sean, Sanchez, Marina Naval, Kube, Peter, King, Harry, Evans, Bradley, Nome, Torfinn, Lien, Sigbjorn and Verbyla, Klara (2018). Evolution of sex determination loci in Atlantic salmon. Scientific Reports, 8 (1) 5664, 5664. doi: 10.1038/s41598-018-23984-1

Mammalian genomic regulatory regions predicted by utilizing human genomics, transcriptomics, and epigenetics data

Nguyen, Quan H., Tellam, Ross L., Naval-Sanchez, Marina, Porto-Neto, Laercio R., Barendse, William, Reverter, Antonio, Hayes, Benjamin, Kijas, James and Dalrymple, Brian P. (2018). Mammalian genomic regulatory regions predicted by utilizing human genomics, transcriptomics, and epigenetics data. Gigascience, 7 (3), 1-17. doi: 10.1093/gigascience/gix136

Sheep genome functional annotation reveals proximal regulatory elements contributed to the evolution of modern breeds

Naval-Sanchez, Marina, Nguyen, Quan, McWilliam, Sean, Porto-Neto, Laercio R., Tellam, Ross, Vuocolo, Tony, Reverter, Antonio, Perez-Enciso, Miguel, Brauning, Rudiger, Clarke, Shannon, McCulloch, Alan, Zamani, Wahid, Naderi, Saeid, Rezaei, Hamid Reza, Pompanon, Francois, Taberlet, Pierre, Worley, Kim C., Gibbs, Richard A., Muzny, Donna M., Jhangiani, Shalini N., Cockett, Noelle, Daetwyler, Hans and Kijas, James (2018). Sheep genome functional annotation reveals proximal regulatory elements contributed to the evolution of modern breeds. Nature Communications, 9 (1) 859. doi: 10.1038/s41467-017-02809-1

Nuclear receptors connect progenitor transcription factors to cell cycle control

Neto, Marta, Naval-Sanchez, Marina, Potier, Delphine, Pereira, Paulo S., Geerts, Dirk, Aerts, Stein and Casares, Fernando (2017). Nuclear receptors connect progenitor transcription factors to cell cycle control. Scientific Reports, 7 (1) 4845, 4845. doi: 10.1038/s41598-017-04936-7

Genome-wide association reveals the locus responsible for four-horned ruminant

Kijas, James W., Hadfield, Tracy, Naval Sanchez, Marina and Cockett, Noelle (2016). Genome-wide association reveals the locus responsible for four-horned ruminant. Animal Genetics, 47 (2), 258-62. doi: 10.1111/age.12409

Identification of lineage-specific Cis-regulatory modules associated with variation in transcription factor binding and chromatin activity using Ornstein-Uhlenbeck models

Naval-Sanchez, Marina, Potier, Delphine, Hulselmans, Gert, Christiaens, Valerie and Aerts, Stein (2015). Identification of lineage-specific Cis-regulatory modules associated with variation in transcription factor binding and chromatin activity using Ornstein-Uhlenbeck models. Molecular Biology and Evolution, 32 (9), 2441-2455. doi: 10.1093/molbev/msv107

Mapping gene regulatory networks in Drosophila eye development by large-scale transcriptome perturbations and motif inference

Potier, Delphine, Davie, Kristofer, Hulselmans, Gert, Sanchez, Marina Naval, Haagen, Lotte, Van Anh Huynh-Thu,, Koldere, Duygu, Celik, Arzu, Geurts, Pierre, Christiaens, Valerie and Aerts, Stein (2014). Mapping gene regulatory networks in Drosophila eye development by large-scale transcriptome perturbations and motif inference. Cell Reports, 9 (6), 2290-2303. doi: 10.1016/j.celrep.2014.11.038

iRegulon: From a gene list to a gene regulatory network using large motif and track collections

Janky, Rekin's, Verfaillie, Annelien, Imrichova, Hana, Van de Sande, Bram, Standaert, Laura, Christiaens, Valerie, Hulselmans, Gert, Herten, Koen, Sanchez, Marina Naval, Potier, Delphine, Svetlichnyy, Dmitry, Atak, Zeynep Kalender, Fiers, Mark, Marine, Jean-Christophe and Aerts, Stein (2014). iRegulon: From a gene list to a gene regulatory network using large motif and track collections. PLOS Computational Biology, 10 (7) ARTN e1003731, e1003731. doi: 10.1371/journal.pcbi.1003731

Comparative motif discovery combined with comparative transcriptomics yields accurate targetome and enhancer predictions

Naval-Sanchez, Marina, Potier, Delphine, Haagen, Lotte, Sanchez, Maximo, Munck, Sebastian, Van de Sande, Bram, Casares, Fernando, Christiaens, Valerie and Aerts, Stein (2013). Comparative motif discovery combined with comparative transcriptomics yields accurate targetome and enhancer predictions. Genome Research, 23 (1), 74-88. doi: 10.1101/gr.140426.112

TDP-43 loss-of-function causes neuronal loss due to defective steroid receptor-mediated gene program switching in Drosophila

Broeck, Lies Vanden, Naval-Sanchez, Marina, Adachi, Yoshitsugu, Diaper, Danielle, Dourlen, Pierre, Chapuis, Julien, Kleinberger, Gernot, Gistelinck, Marc, Van Broeckhoven, Christine, Lambert, Jean-Charles, Hirth, Frank, Aerts, Stein, Callaerts, Patrick and Dermaut, Bart (2013). TDP-43 loss-of-function causes neuronal loss due to defective steroid receptor-mediated gene program switching in Drosophila. Cell Reports, 3 (1), 160-172. doi: 10.1016/j.celrep.2012.12.014

Robust target gene discovery through transcriptome perturbations and genome-wide enhancer predictions in drosophila uncovers a regulatory basis for sensory specification

Aerts, Stein, Quan, Xiao-Jiang, Claeys, Annelies, Sanchez, Marina Naval, Tate, Phillip, Yan, Jiekun and Hassan, Bassem A. (2010). Robust target gene discovery through transcriptome perturbations and genome-wide enhancer predictions in drosophila uncovers a regulatory basis for sensory specification. PLoS Biology, 8 (7) ARTN e1000435, e1000435. doi: 10.1371/journal.pbio.1000435

Measurement of free zinc concentration in wine with AGNES

Companys, Encarnacio, Naval-Sanchez, Marina, Martinez-Micaelo, Neus, Puy, Jaume and Galceran, Josep (2008). Measurement of free zinc concentration in wine with AGNES. Journal of Agricultural and Food Chemistry, 56 (18), 8296-8302. doi: 10.1021/jf8013475

Chromatin accessibility and regulatory vocabulary in indicine cattle

Alexandre, Pâmela A., Naval-Sánchez, Marina, Menzies, Moira, Nguyen, Loan T., Porto-Neto, Laercio, Fortes, Marina R.S. and Reverter, Antonio (2021). Chromatin accessibility and regulatory vocabulary in indicine cattle. 38th International Society of Animal Genetics (ISAG), Virtual, 26-30 July 2021. Champaign, IL United States: ISAG.