Browsing by Author "Gehlenborg, Nils"

Now showing 1 - 4 of 4
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    Highlights from the Fourth International Society for Computational Biology Student Council Symposium at the Sixteenth Annual International Conference on Intelligent Systems for Molecular Biology
    (2008-10) Peixoto, Lucia; Gehlenborg, Nils; Janga, Sarath Chandra
    In this meeting report we give an overview of the talks and presentations from the Fourth International Society for Computational Biology (ISCB) Student Council Symposium held as part of the annual Intelligent Systems for Molecular Biology (ISMB) conference in Toronto, Canada. Furthermore, we detail the role of the Student Council (SC) as an international student body in organizing this symposium series in the context of large, international conferences.
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    Highlights from the Third International Society for Computational Biology Student Council Symposium at the Fifteenth Annual International Conference on Intelligent Systems for Molecular Biology
    (2007-11) Gehlenborg, Nils; Corpas, Manuel; Janga, Sarath Chandra
    In this meeting report we give an overview of the 3rd International Society for Computational Biology Student Council Symposium. Furthermore, we explain the role of the Student Council and the symposium series in the context of large, international conferences.
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    Ten Simple Rules for Organizing a Scientific Meeting
    (2008-06) Corpas, Manuel; Gehlenborg, Nils; Janga, Sarath Chandra; Bourne, Philip E.
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    The chromatin landscape of healthy and injured cell types in the human kidney
    (Springer Nature, 2024-01-10) Gisch, Debora L.; Brennan, Michelle; Lake, Blue B.; Basta, Jeannine; Keller, Mark S.; Ferreira, Ricardo Melo; Akilesh, Shreeram; Ghag, Reetika; Lu, Charles; Cheng, Ying-Hua; Collins, Kimberly S.; Parikh, Samir V.; Rovin, Brad H.; Robbins, Lynn; Stout, Lisa; Conklin, Kimberly Y.; Diep, Dinh; Zhang, Bo; Knoten, Amanda; Barwinska, Daria; Asghari, Mahla; Sabo, Angela R.; Ferkowicz, Michael J.; Sutton, Timothy A.; Kelly, Katherine J.; De Boer, Ian H.; Rosas, Sylvia E.; Kiryluk, Krzysztof; Hodgin, Jeffrey B.; Alakwaa, Fadhl; Winfree, Seth; Jefferson, Nichole; Türkmen, Aydın; Gaut, Joseph P.; Gehlenborg, Nils; Phillips, Carrie L.; El-Achkar, Tarek M.; Dagher, Pierre C.; Hato, Takashi; Zhang, Kun; Himmelfarb, Jonathan; Kretzler, Matthias; Mollah, Shamim; Kidney Precision Medicine Project (KPMP); Jain, Sanjay; Rauchman, Michael; Eadon, Michael T.; Medicine, School of Medicine
    There is a need to define regions of gene activation or repression that control human kidney cells in states of health, injury, and repair to understand the molecular pathogenesis of kidney disease and design therapeutic strategies. Comprehensive integration of gene expression with epigenetic features that define regulatory elements remains a significant challenge. We measure dual single nucleus RNA expression and chromatin accessibility, DNA methylation, and H3K27ac, H3K4me1, H3K4me3, and H3K27me3 histone modifications to decipher the chromatin landscape and gene regulation of the kidney in reference and adaptive injury states. We establish a spatially-anchored epigenomic atlas to define the kidney's active, silent, and regulatory accessible chromatin regions across the genome. Using this atlas, we note distinct control of adaptive injury in different epithelial cell types. A proximal tubule cell transcription factor network of ELF3, KLF6, and KLF10 regulates the transition between health and injury, while in thick ascending limb cells this transition is regulated by NR2F1. Further, combined perturbation of ELF3, KLF6, and KLF10 distinguishes two adaptive proximal tubular cell subtypes, one of which manifested a repair trajectory after knockout. This atlas will serve as a foundation to facilitate targeted cell-specific therapeutics by reprogramming gene regulatory networks.