DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation
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
Published in eLife (05.05.2015)
Published in eLife (05.05.2015)
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Journal Article
A linear mixed-model approach to study multivariate gene-environment interactions
Moore, Rachel, Casale, Francesco Paolo, Jan Bonder, Marc, Horta, Danilo, Franke, Lude, Barroso, Inês, Stegle, Oliver
Published in Nature genetics (01.01.2019)
Published in Nature genetics (01.01.2019)
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Journal Article
Joint genetic analysis using variant sets reveals polygenic gene-context interactions
Casale, Francesco Paolo, Horta, Danilo, Rakitsch, Barbara, Stegle, Oliver
Published in PLoS genetics (20.04.2017)
Published in PLoS genetics (20.04.2017)
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Journal Article
Genetic Variation in the Social Environment Contributes to Health and Disease
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
Published in PLoS genetics (01.01.2017)
Published in PLoS genetics (01.01.2017)
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Journal Article
The germline genetic component of drug sensitivity in cancer cell lines
Menden, Michael P, Casale, Francesco Paolo, Stephan, Johannes, Bignell, Graham R, Iorio, Francesco, McDermott, Ultan, Garnett, Mathew J, Saez-Rodriguez, Julio, Stegle, Oliver
Published in Nature communications (23.08.2018)
Published in Nature communications (23.08.2018)
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Journal Article
Dissecting indirect genetic effects from peers in laboratory mice
Baud, Amelie, Casale, Francesco Paolo, Barkley-Levenson, Amanda M, Farhadi, Nilgoun, Montillot, Charlotte, Yalcin, Binnaz, Nicod, Jerome, Palmer, Abraham A, Stegle, Oliver
Published in Genome Biology (26.07.2021)
Published in Genome Biology (26.07.2021)
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Journal Article
Population-scale proteome variation in human induced pluripotent stem cells
Mirauta, Bogdan Andrei, Seaton, Daniel D, Bensaddek, Dalila, Brenes, Alejandro, Bonder, Marc Jan, Kilpinen, Helena, Stegle, Oliver, Lamond, Angus I
Published in eLife (10.08.2020)
Published in eLife (10.08.2020)
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Journal Article
Single-cell states in the estrogen response of breast cancer cell lines
Casale, Francesco Paolo, Giurato, Giorgio, Nassa, Giovanni, Armond, Jonathan W, Oates, Chris J, Corá, Davide, Gamba, Andrea, Mukherjee, Sach, Weisz, Alessandro, Nicodemi, Mario
Published in PloS one (25.02.2014)
Published in PloS one (25.02.2014)
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Journal Article
기계 학습 모델을 사용한 질환 결과 예측
PALMEDO PETER FRANKLIN JR, SULTAN MOHAMMAD MUNEEB, RIESSELMAN ADAM JOSEPH, COTTA RAMUSINO CECILIA GIOVANNA SILVIA, SALICK MAX R, SHARON EILON, CASALE FRANCESCO PAOLO, KATEGAYA LORN, STANITSAS PANAGIOTIS DIMITRIOS, KOLLER DAPHNE, KAYKAS AJAMETE
Year of Publication 31.01.2023
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Year of Publication 31.01.2023
Patent
Efficient set tests for the genetic analysis of correlated traits
Casale, Francesco Paolo, Rakitsch, Barbara, Lippert, Christoph, Stegle, Oliver
Published in Nature methods (01.08.2015)
Published in Nature methods (01.08.2015)
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Journal Article
Genetics-driven risk predictions leveraging the Mendelian randomization framework
Sens, Daniel, Shilova, Liubov, Gräf, Ludwig, Grebenshchikova, Maria, Eskofier, Bjoern M, Casale, Francesco Paolo
Published in Genome research (27.09.2024)
Published in Genome research (27.09.2024)
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Journal Article
Common genetic variation drives molecular heterogeneity in human iPSCs
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
Published in Nature (London) (15.06.2017)
Published in Nature (London) (15.06.2017)
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Journal Article
Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells
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
Published in Cell (17.11.2016)
Published in Cell (17.11.2016)
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Journal Article
Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression
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
Published in Nature communications (10.02.2020)
Published in Nature communications (10.02.2020)
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Journal Article
An allelic-series rare-variant association test for candidate-gene discovery
McCaw, Zachary R., O’Dushlaine, Colm, Somineni, Hari, Bereket, Michael, Klein, Christoph, Karaletsos, Theofanis, Casale, Francesco Paolo, Koller, Daphne, Soare, Thomas W.
Published in American journal of human genetics (03.08.2023)
Published in American journal of human genetics (03.08.2023)
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Journal Article
Machine learning methods for detailed characterization of TGF-beta-induced signatures in a large iPSC-derived hepatic stellate cell cohort
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
Published in Journal of hepatology (01.07.2022)
Published in Journal of hepatology (01.07.2022)
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Journal Article
Machine learning encoding of liver biopsy images enables prediction of molecular measurements in a NASH F3/F4 fibrosis clinical cohort
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
Published in Journal of hepatology (01.07.2022)
Published in Journal of hepatology (01.07.2022)
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Journal Article
Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types
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
Published in Genome Biology (26.01.2017)
Published in Genome Biology (26.01.2017)
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Journal Article