iRegulon: from a gene list to a gene regulatory network using large motif and track collections von Janky, Rekin's, Verfaillie, Annelien, Imrichová, Hana, Van de Sande, Bram, Standaert, Laura, Christiaens, Valerie, Hulselmans, Gert, Herten, Koen, Naval Sanchez, Marina, Potier, Delphine, Svetlichnyy, Dmitry, Kalender Atak, Zeynep, Fiers, Mark, Marine, Jean-Christophe, Aerts, Stein

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Evolution of Sex Determination Loci in Atlantic Salmon von Kijas, James, McWilliam, Sean, Naval Sanchez, Marina, Kube, Peter, King, Harry, Evans, Bradley, Nome, Torfinn, Lien, Sigbjørn, Verbyla, Klara

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Mapping Gene Regulatory Networks in Drosophila Eye Development by Large-Scale Transcriptome Perturbations and Motif Inference von Potier, Delphine, Davie, Kristofer, Hulselmans, Gert, Naval Sanchez, Marina, Haagen, Lotte, Huynh-Thu, Vân Anh, Koldere, Duygu, Celik, Arzu, Geurts, Pierre, Christiaens, Valerie, Aerts, Stein

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Robust target gene discovery through transcriptome perturbations and genome-wide enhancer predictions in Drosophila uncovers a regulatory basis for sensory specification von Aerts, Stein, Quan, Xiao-Jiang, Claeys, Annelies, Naval Sanchez, Marina, Tate, Phillip, Yan, Jiekun, Hassan, Bassem A

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Organization of gene programs revealed by unsupervised analysis of diverse gene–trait associations von Mizikovsky, Dalia, Naval Sanchez, Marina, Nefzger, Christian M, Cuellar Partida, Gabriel, Palpant, Nathan J

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Nicotinamide riboside attenuates age-associated metabolic and functional changes in hematopoietic stem cells von 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., Nilsson, Susan K.

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Sheep genome functional annotation reveals proximal regulatory elements contributed to the evolution of modern breeds von 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, Kijas, James

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Leveraging transcriptome and epigenome landscapes to infer regulatory networks during the onset of sexual maturation von Mohamed, Amin R, Naval-Sanchez, Marina, Menzies, Moira, Evans, Bradley, King, Harry, Reverter, Antonio, Kijas, James W

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Chromatin accessibility and regulatory vocabulary across indicine cattle tissues von Alexandre, Pâmela A, Naval-Sánchez, Marina, Menzies, Moira, Nguyen, Loan T, Porto-Neto, Laercio R, Fortes, Marina R S, Reverter, Antonio

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Micrococcal nuclease sequencing of porcine sperm suggests enriched co-location between retained histones and genomic regions related to semen quality and early embryo development von Gòdia, Marta, Lian, Yu, Naval-Sanchez, Marina, Ponte, Inma, Rodríguez-Gil, Joan Enric, Sanchez, Armand, Clop, Alex

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Systems Biology Reveals NR2F6 and TGFB1 as Key Regulators of Feed Efficiency in Beef Cattle von Alexandre, Pâmela A, Naval-Sanchez, Marina, Porto-Neto, Laercio R, Ferraz, José Bento S, Reverter, Antonio, Fukumasu, Heidge

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Changed Patterns of Genomic Variation Following Recent Domestication: Selection Sweeps in Farmed Atlantic Salmon von Naval-Sanchez, Marina, McWilliam, Sean, Evans, Bradley, Yáñez, José M, Houston, Ross D, Kijas, James W

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Temporal perturbation of histone deacetylase activity reveals a requirement for HDAC1–3 in mesendoderm cell differentiation von 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., Palpant, Nathan J.

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Dynamics of Gene Co-expression Networks in Time-Series Data: A Case Study in Drosophila melanogaster Embryogenesis von Lau, Li Yieng, Reverter, Antonio, Hudson, Nicholas J., Naval-Sanchez, Marina, Fortes, Marina R. S., Alexandre, Pâmela A.

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Benchmarking of ATAC Sequencing Data From BGI's Low-Cost DNBSEQ-G400 Instrument for Identification of Open and Occupied Chromatin Regions von Naval-Sanchez, Marina, Deshpande, Nikita, Tran, Minh, Zhang, Jingyu, Alhomrani, Majid, Alsanie, Walaa, Nguyen, Quan, Nefzger, Christian M

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Nuclear receptors connect progenitor transcription factors to cell cycle control von Neto, Marta, Naval-Sánchez, Marina, Potier, Delphine, Pereira, Paulo S., Geerts, Dirk, Aerts, Stein, Casares, Fernando

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Comparative motif discovery combined with comparative transcriptomics yields accurate targetome and enhancer predictions von Naval-Sánchez, Marina, Potier, Delphine, Haagen, Lotte, Sánchez, Máximo, Munck, Sebastian, Van de Sande, Bram, Casares, Fernando, Christiaens, Valerie, Aerts, Stein

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TDP-43 Loss-of-Function Causes Neuronal Loss Due to Defective Steroid Receptor-Mediated Gene Program Switching in Drosophila von Vanden Broeck, Lies, Naval-Sánchez, 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, Dermaut, Bart

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Measurement of Free Zinc Concentration in Wine with AGNES von Companys, Encarnació, Naval-Sánchez, Marina, Martínez-Micaelo, Neus, Puy, Jaume, Galceran, Josep

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Identification of Lineage-Specific Cis-Regulatory Modules Associated with Variation in Transcription Factor Binding and Chromatin Activity Using Ornstein-Uhlenbeck Models von Naval-Sánchez, Marina, Potier, Delphine, Hulselmans, Gert, Christiaens, Valerie, Aerts, Stein

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