Search Results - "Paolo Casale, Francesco"

DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation by Dubin, Manu J, Zhang, Pei, Meng, Dazhe, Remigereau, Marie-Stanislas, Osborne, Edward J, Paolo Casale, Francesco, Drewe, Philipp, Kahles, André, Jean, Geraldine, Vilhjálmsson, Bjarni, Jagoda, Joanna, Irez, Selen, Voronin, Viktor, Song, Qiang, Long, Quan, Rätsch, Gunnar, Stegle, Oliver, Clark, Richard M, Nordborg, Magnus

“…Epigenome modulation potentially provides a mechanism for organisms to adapt, within and between generations. However, neither the extent to which this occurs,…”
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A linear mixed-model approach to study multivariate gene–environment interactions by Moore, Rachel, Casale, Francesco Paolo, Jan Bonder, Marc, Horta, Danilo, Franke, Lude, Barroso, Inês, Stegle, Oliver

“…Different exposures, including diet, physical activity, or external conditions can contribute to genotype–environment interactions (G×E). Although…”
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Joint genetic analysis using variant sets reveals polygenic gene-context interactions by Casale, Francesco Paolo, Horta, Danilo, Rakitsch, Barbara, Stegle, Oliver

“…Joint genetic models for multiple traits have helped to enhance association analyses. Most existing multi-trait models have been designed to increase power for…”
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Genetic Variation in the Social Environment Contributes to Health and Disease by Baud, Amelie, Mulligan, Megan K, Casale, Francesco Paolo, Ingels, Jesse F, Bohl, Casey J, Callebert, Jacques, Launay, Jean-Marie, Krohn, Jon, Legarra, Andres, Williams, Robert W, Stegle, Oliver

“…Assessing the impact of the social environment on health and disease is challenging. As social effects are in part determined by the genetic makeup of social…”
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The germline genetic component of drug sensitivity in cancer cell lines by Menden, Michael P., Casale, Francesco Paolo, Stephan, Johannes, Bignell, Graham R., Iorio, Francesco, McDermott, Ultan, Garnett, Mathew J., Saez-Rodriguez, Julio, Stegle, Oliver

“…Patients with seemingly the same tumour can respond very differently to treatment. There are strong, well-established effects of somatic mutations on drug…”
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Dissecting indirect genetic effects from peers in laboratory mice by Baud, Amelie, Casale, Francesco Paolo, Barkley-Levenson, Amanda M, Farhadi, Nilgoun, Montillot, Charlotte, Yalcin, Binnaz, Nicod, Jerome, Palmer, Abraham A, Stegle, Oliver

“…The phenotype of an individual can be affected not only by the individual's own genotypes, known as direct genetic effects (DGE), but also by genotypes of…”
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Population-scale proteome variation in human induced pluripotent stem cells by Mirauta, Bogdan Andrei, Seaton, Daniel D, Bensaddek, Dalila, Brenes, Alejandro, Bonder, Marc Jan, Kilpinen, Helena, Stegle, Oliver, Lamond, Angus I

“…Human disease phenotypes are driven primarily by alterations in protein expression and/or function. To date, relatively little is known about the variability…”
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Single-cell states in the estrogen response of breast cancer cell lines by Casale, Francesco Paolo, Giurato, Giorgio, Nassa, Giovanni, Armond, Jonathan W, Oates, Chris J, Corá, Davide, Gamba, Andrea, Mukherjee, Sach, Weisz, Alessandro, Nicodemi, Mario

“…Estrogen responsive breast cancer cell lines have been extensively studied to characterize transcriptional patterns in hormone-responsive tumors. Nevertheless,…”
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Efficient set tests for the genetic analysis of correlated traits by Casale, Francesco Paolo, Rakitsch, Barbara, Lippert, Christoph, Stegle, Oliver

“…The multi-trait set test (mtSet) is an efficient mixed-model method that enables genome-wide association tests for large cohorts and multiple quantitative…”
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Genetics-driven risk predictions leveraging the Mendelian randomization framework by Sens, Daniel, Shilova, Liubov, Gräf, Ludwig, Grebenshchikova, Maria, Eskofier, Bjoern M, Casale, Francesco Paolo

“…Accurate predictive models of future disease onset are crucial for effective preventive healthcare, yet longitudinal data sets linking early risk factors to…”
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Common genetic variation drives molecular heterogeneity in human iPSCs by Kilpinen, Helena, Goncalves, Angela, Leha, Andreas, Afzal, Vackar, Alasoo, Kaur, Ashford, Sofie, Bala, Sendu, Bensaddek, Dalila, Casale, Francesco Paolo, Culley, Oliver J., Danecek, Petr, Faulconbridge, Adam, Harrison, Peter W., Kathuria, Annie, McCarthy, Davis, McCarthy, Shane A., Meleckyte, Ruta, Memari, Yasin, Moens, Nathalie, Soares, Filipa, Mann, Alice, Streeter, Ian, Agu, Chukwuma A., Alderton, Alex, Nelson, Rachel, Harper, Sarah, Patel, Minal, White, Alistair, Patel, Sharad R., Clarke, Laura, Halai, Reena, Kirton, Christopher M., Kolb-Kokocinski, Anja, Beales, Philip, Birney, Ewan, Danovi, Davide, Lamond, Angus I., Ouwehand, Willem H., Vallier, Ludovic, Watt, Fiona M., Durbin, Richard, Stegle, Oliver, Gaffney, Daniel J.

“…Technology utilizing human induced pluripotent stem cells (iPS cells) has enormous potential to provide improved cellular models of human disease. However,…”
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Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells by Chen, Lu, Ge, Bing, Casale, Francesco Paolo, Vasquez, Louella, Kwan, Tony, Garrido-Martín, Diego, Watt, Stephen, Yan, Ying, Kundu, Kousik, Ecker, Simone, Datta, Avik, Richardson, David, Burden, Frances, Mead, Daniel, Mann, Alice L., Fernandez, Jose Maria, Rowlston, Sophia, Wilder, Steven P., Farrow, Samantha, Shao, Xiaojian, Lambourne, John J., Redensek, Adriana, Albers, Cornelis A., Amstislavskiy, Vyacheslav, Ashford, Sofie, Berentsen, Kim, Bomba, Lorenzo, Bourque, Guillaume, Bujold, David, Busche, Stephan, Caron, Maxime, Chen, Shu-Huang, Cheung, Warren, Delaneau, Oliver, Dermitzakis, Emmanouil T., Elding, Heather, Colgiu, Irina, Bagger, Frederik O., Flicek, Paul, Habibi, Ehsan, Iotchkova, Valentina, Janssen-Megens, Eva, Kim, Bowon, Lehrach, Hans, Lowy, Ernesto, Mandoli, Amit, Matarese, Filomena, Maurano, Matthew T., Morris, John A., Pancaldi, Vera, Pourfarzad, Farzin, Rehnstrom, Karola, Rendon, Augusto, Risch, Thomas, Sharifi, Nilofar, Simon, Marie-Michelle, Sultan, Marc, Valencia, Alfonso, Walter, Klaudia, Wang, Shuang-Yin, Frontini, Mattia, Antonarakis, Stylianos E., Clarke, Laura, Yaspo, Marie-Laure, Beck, Stephan, Guigo, Roderic, Rico, Daniel, Martens, Joost H.A., Ouwehand, Willem H., Kuijpers, Taco W., Paul, Dirk S., Stunnenberg, Hendrik G., Stegle, Oliver, Downes, Kate, Pastinen, Tomi, Soranzo, Nicole

“…Characterizing the multifaceted contribution of genetic and epigenetic factors to disease phenotypes is a major challenge in human genetics and medicine. We…”
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Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression by Cuomo, Anna S. E., Seaton, Daniel D., McCarthy, Davis J., Martinez, Iker, Bonder, Marc Jan, Garcia-Bernardo, Jose, Amatya, Shradha, Madrigal, Pedro, Isaacson, Abigail, Buettner, Florian, Knights, Andrew, Natarajan, Kedar Nath, Vallier, Ludovic, Marioni, John C., Chhatriwala, Mariya, Stegle, Oliver

“…Recent developments in stem cell biology have enabled the study of cell fate decisions in early human development that are impossible to study in vivo…”
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An allelic-series rare-variant association test for candidate-gene discovery by McCaw, Zachary R., O’Dushlaine, Colm, Somineni, Hari, Bereket, Michael, Klein, Christoph, Karaletsos, Theofanis, Casale, Francesco Paolo, Koller, Daphne, Soare, Thomas W.

“…Allelic series are of candidate therapeutic interest because of the existence of a dose-response relationship between the functionality of a gene and the…”
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Machine learning encoding of liver biopsy images enables prediction of molecular measurements in a NASH F3/F4 fibrosis clinical cohort by Bereket, Michael D., Casale, Francesco Paolo, Loomba, Rohit, Sanyal, Arun, Harrison, Stephen, Younossi, Zobair, Jia, Catherine, Lopez, David, Li, Li, Myers, Robert, Breckinridge, David, Billin, Andrew, Sharon, Eilon, Albert, Matthew, Karaletsos, Theofanis, Koller, Daphne

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Machine learning methods for detailed characterization of TGF-beta-induced signatures in a large iPSC-derived hepatic stellate cell cohort by Stanitsas, Panagiotis, Liu, Kara Marie, Kategaya, Lorn, Haston, Kelly, Lee, Alicia, Mohammadi, Shahin, Zheng, Haoyang, Casale, Francesco Paolo, Ranu, Navpreet, Sandakli, Ahmed, Prasad, Pooja, Chen, Owen, Baldwin, Anne, Kim, Albert, Sharon, Eilon, Kaykas, Ajamete, Koller, Daphne, Albert, Matthew

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Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types by Ecker, Simone, Chen, Lu, Pancaldi, Vera, Bagger, Frederik O, Fernández, José María, Carrillo de Santa Pau, Enrique, Juan, David, Mann, Alice L, Watt, Stephen, Casale, Francesco Paolo, Sidiropoulos, Nikos, Rapin, Nicolas, Merkel, Angelika, Stunnenberg, Hendrik G, Stegle, Oliver, Frontini, Mattia, Downes, Kate, Pastinen, Tomi, Kuijpers, Taco W, Rico, Daniel, Valencia, Alfonso, Beck, Stephan, Soranzo, Nicole, Paul, Dirk S

“…A healthy immune system requires immune cells that adapt rapidly to environmental challenges. This phenotypic plasticity can be mediated by transcriptional and…”
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BEL: A Bag Embedding Loss for Transformer Enhances Multiple Instance Whole Slide Image Classification by Sens, Daniel, Sadafi, Ario, Casale, Francesco Paolo, Navab, Nassir, Marr, Carsten

“…Multiple Instance Learning (MIL) has become the predominant approach for classification tasks on gigapixel histopathology whole slide images (WSIs). Within the…”
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SCAS dashboard: A tool to intuitively and interactively analyze Slurm cluster usage by Walzthoeni, Thomas, Singiali, Bom Bahadur, Rayner, N. William, Casale, Francesco Paolo, Feest, Christoph, Marr, Carsten, Wachsmann, Alf

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Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes by McCarthy, Davis J., Rostom, Raghd, Huang, Yuanhua, Kunz, Daniel J., Danecek, Petr, Bonder, Marc Jan, Hagai, Tzachi, Lyu, Ruqian, Wang, Wenyi, Gaffney, Daniel J., Simons, Benjamin D., Stegle, Oliver, Teichmann, Sarah A.

“…Bulk and single-cell DNA sequencing has enabled reconstructing clonal substructures of somatic tissues from frequency and cooccurrence patterns of somatic…”
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