Subtle changes in chromatin loop contact propensity are associated with differential gene regulation and expression von Greenwald, William W., Li, He, Benaglio, Paola, Jakubosky, David, Matsui, Hiroko, Schmitt, Anthony, Selvaraj, Siddarth, D’Antonio, Matteo, D’Antonio-Chronowska, Agnieszka, Smith, Erin N., Frazer, Kelly A.

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Large-Scale Profiling Reveals the Influence of Genetic Variation on Gene Expression in Human Induced Pluripotent Stem Cells von DeBoever, Christopher, Li, He, Jakubosky, David, Benaglio, Paola, Reyna, Joaquin, Olson, Katrina M., Huang, Hui, Biggs, William, Sandoval, Efren, D’Antonio, Matteo, Jepsen, Kristen, Matsui, Hiroko, Arias, Angelo, Ren, Bing, Nariai, Naoki, Smith, Erin N., D’Antonio-Chronowska, Agnieszka, Farley, Emma K., Frazer, Kelly A.

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Mapping genetic effects on cell type-specific chromatin accessibility and annotating complex immune trait variants using single nucleus ATAC-seq in peripheral blood von Benaglio, Paola, Newsome, Jacklyn, Han, Jee Yun, Chiou, Joshua, Aylward, Anthony, Corban, Sierra, Miller, Michael, Okino, Mei-Lin, Kaur, Jaspreet, Preissl, Sebastian, Gorkin, David U, Gaulton, Kyle J

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Glucocorticoid signaling in pancreatic islets modulates gene regulatory programs and genetic risk of type 2 diabetes von Aylward, Anthony, Okino, Mei-Lin, Benaglio, Paola, Chiou, Joshua, Beebe, Elisha, Padilla, Jose Andres, Diep, Sharlene, Gaulton, Kyle J

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Pgltools: a genomic arithmetic tool suite for manipulation of Hi-C peak and other chromatin interaction data von Greenwald, William W, Li, He, Smith, Erin N, Benaglio, Paola, Nariai, Naoki, Frazer, Kelly A

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FOXO1 mitigates the SMAD3/FOXL2C134W transcriptomic effect in a model of human adult granulosa cell tumor von Secchi, Christian, Benaglio, Paola, Mulas, Francesca, Belli, Martina, Stupack, Dwayne, Shimasaki, Shunichi

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Whole genome sequencing in patients with retinitis pigmentosa reveals pathogenic DNA structural changes and NEK2 as a new disease gene von Nishiguchi, Koji M., Tearle, Richard G., Liu, Yangfan P., Oh, Edwin C., Miyake, Noriko, Benaglio, Paola, Harper, Shyana, Koskiniemi-Kuendig, Hanna, Venturini, Giulia, Sharon, Dror, Koenekoop, Robert K., Nakamura, Makoto, Kondo, Mineo, Ueno, Shinji, Yasuma, Tetsuhiro R., Beckmann, Jacques S., Ikegawa, Shiro, Matsumoto, Naomichi, Terasaki, Hiroko, Berson, Eliot L., Katsanis, Nicholas, Rivolta, Carlo

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Human iPSC-Derived Retinal Pigment Epithelium: A Model System for Prioritizing and Functionally Characterizing Causal Variants at AMD Risk Loci von Smith, Erin N., D'Antonio-Chronowska, Agnieszka, Greenwald, William W., Borja, Victor, Aguiar, Lana R., Pogue, Robert, Matsui, Hiroko, Benaglio, Paola, Borooah, Shyamanga, D'Antonio, Matteo, Ayyagari, Radha, Frazer, Kelly A.

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Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds von Miyazaki, Ryo, Bertelli, Claire, Benaglio, Paola, Canton, Jonas, De Coi, Nicoló, Gharib, Walid H., Gjoksi, Bebeka, Goesmann, Alexander, Greub, Gilbert, Harshman, Keith, Linke, Burkhard, Mikulic, Josip, Mueller, Linda, Nicolas, Damien, Robinson-Rechavi, Marc, Rivolta, Carlo, Roggo, Clémence, Roy, Shantanu, Sentchilo, Vladimir, Siebenthal, Alexandra Von, Falquet, Laurent, van der Meer, Jan Roelof

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Ultra high throughput sequencing in human DNA variation detection: a comparative study on the NDUFA3-PRPF31 region von Benaglio, Paola, Rivolta, Carlo

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Target Sequencing, Cell Experiments, and a Population Study Establish Endothelial Nitric Oxide Synthase (eNOS) Gene as Hypertension Susceptibility Gene von Salvi, Erika, Kuznetsova, Tatiana, Thijs, Lutgarde, Lupoli, Sara, Stolarz-Skrzypek, Katarzyna, D’Avila, Francesca, Tikhonoff, Valerie, De Astis, Silvia, Barcella, Matteo, Seidlerová, Jitka, Benaglio, Paola, Malyutina, Sofia, Frau, Francesca, Velayutham, Dinesh, Benfante, Roberta, Zagato, Laura, Title, Alexandra, Braga, Daniele, Marek, Diana, Kawecka-Jaszcz, Kalina, Casiglia, Edoardo, Filipovský, Jan, Nikitin, Yuri, Rivolta, Carlo, Manunta, Paolo, Beckmann, Jacques S, Barlassina, Cristina, Cusi, Daniele, Staessen, Jan A

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Network-guided analysis of genes with altered somatic copy number and gene expression reveals pathways commonly perturbed in metastatic melanoma von Valsesia, Armand, Rimoldi, Donata, Martinet, Danielle, Ibberson, Mark, Benaglio, Paola, Quadroni, Manfredo, Waridel, Patrice, Gaillard, Muriel, Pidoux, Mireille, Rapin, Blandine, Rivolta, Carlo, Xenarios, Ioannis, Simpson, Andrew J G, Antonarakis, Stylianos E, Beckmann, Jacques S, Jongeneel, C Victor, Iseli, Christian, Stevenson, Brian J

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Interpreting type 1 diabetes risk with genetics and single-cell epigenomics von Chiou, Joshua, Geusz, Ryan J., Okino, Mei-Lin, Han, Jee Yun, Miller, Michael, Melton, Rebecca, Beebe, Elisha, Benaglio, Paola, Huang, Serina, Korgaonkar, Katha, Heller, Sandra, Kleger, Alexander, Preissl, Sebastian, Gorkin, David U., Sander, Maike, Gaulton, Kyle J.

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1267-P: Fine-Mapping Type 1 Diabetes Risk at the MHC Locus von MCGRAIL, CAROLYN, CHIOU, JOSHUA, BENAGLIO, PAOLA, GAULTON, KYLE J.

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Systematic analysis of binding of transcription factors to noncoding variants von Yan, Jian, Qiu, Yunjiang, Ribeiro dos Santos, André M., Yin, Yimeng, Li, Yang E., Vinckier, Nick, Nariai, Naoki, Benaglio, Paola, Raman, Anugraha, Li, Xiaoyu, Fan, Shicai, Chiou, Joshua, Chen, Fulin, Frazer, Kelly A., Gaulton, Kyle J., Sander, Maike, Taipale, Jussi, Ren, Bing

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An Integrated Map of Cell Type-Specific Gene Expression in Pancreatic Islets von Elgamal, Ruth M, Kudtarkar, Parul, Melton, Rebecca L, Mummey, Hannah M, Benaglio, Paola, Okino, Mei-Lin, Gaulton, Kyle J

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Complex regulatory networks influence pluripotent cell state transitions in human iPSCs von Arthur, Timothy D., Nguyen, Jennifer P., D’Antonio-Chronowska, Agnieszka, Matsui, Hiroko, Silva, Nayara S., Joshua, Isaac N., Luchessi, André D., Greenwald, William W. Young, D’Antonio, Matteo, Pera, Martin F., Frazer, Kelly A.

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Insights into the Mutational Burden of Human Induced Pluripotent Stem Cells from an Integrative Multi-Omics Approach von D’Antonio, Matteo, Benaglio, Paola, Jakubosky, David, Greenwald, William W., Matsui, Hiroko, Donovan, Margaret K.R., Li, He, Smith, Erin N., D’Antonio-Chronowska, Agnieszka, Frazer, Kelly A.

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eQTL mapping in fetal-like pancreatic progenitor cells reveals early developmental insights into diabetes risk von Nguyen, Jennifer P., Arthur, Timothy D., Fujita, Kyohei, Salgado, Bianca M., Donovan, Margaret K. R., Matsui, Hiroko, Kim, Ji Hyun, D’Antonio-Chronowska, Agnieszka, D’Antonio, Matteo, Frazer, Kelly A.

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135-OR: Mapping Cis-Regulatory Programs Affecting Diabetes Risk in Pancreatic Islet Cell Types Using Single-Cell Multimodal Profiling von MUMMEY, HANNAH, ELISON, WESTON, KORGAONKAR, KATHA, LEE, YUN S., NEWSOME ASHMUS, JACKLYN M., BENAGLIO, PAOLA, MILLER, MICHAEL T., MANNING FOX, JOCELYN E., GLOYN, ANNA L., MACDONALD, PATRICK, PREISSL, SEBASTIAN, GAULTON, KYLE J.

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