Large-Scale Profiling Reveals the Influence of Genetic Variation on Gene Expression in Human Induced Pluripotent Stem Cells
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.
Published in Cell stem cell (06.04.2017)
Published in Cell stem cell (06.04.2017)
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Systematic genetic analysis of the MHC region reveals mechanistic underpinnings of HLA type associations with disease
D'Antonio, Matteo, Reyna, Joaquin, Jakubosky, David, Donovan, Margaret Kr, Bonder, Marc-Jan, Matsui, Hiroko, Stegle, Oliver, Nariai, Naoki, D'Antonio-Chronowska, Agnieszka, Frazer, Kelly A
Published in eLife (20.11.2019)
Published in eLife (20.11.2019)
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iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types
Panopoulos, Athanasia D., D'Antonio, Matteo, Benaglio, Paola, Williams, Roy, Hashem, Sherin I., Schuldt, Bernhard M., DeBoever, Christopher, Arias, Angelo D., Garcia, Melvin, Nelson, Bradley C., Harismendy, Olivier, Jakubosky, David A., Donovan, Margaret K.R., Greenwald, William W., Farnam, KathyJean, Cook, Megan, Borja, Victor, Miller, Carl A., Grinstein, Jonathan D., Drees, Frauke, Okubo, Jonathan, Diffenderfer, Kenneth E., Hishida, Yuriko, Modesto, Veronica, Dargitz, Carl T., Feiring, Rachel, Zhao, Chang, Aguirre, Aitor, McGarry, Thomas J., Matsui, Hiroko, Li, He, Reyna, Joaquin, Rao, Fangwen, O'Connor, Daniel T., Yeo, Gene W., Evans, Sylvia M., Chi, Neil C., Jepsen, Kristen, Nariai, Naoki, Müller, Franz-Josef, Goldstein, Lawrence S.B., Izpisua Belmonte, Juan Carlos, Adler, Eric, Loring, Jeanne F., Berggren, W. Travis, D'Antonio-Chronowska, Agnieszka, Smith, Erin N., Frazer, Kelly A.
Published in Stem cell reports (11.04.2017)
Published in Stem cell reports (11.04.2017)
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Rewiring of the 3D genome during acquisition of carboplatin resistance in a triple-negative breast cancer patient-derived xenograft
Dozmorov, Mikhail G, Marshall, Maggie A, Rashid, Narmeen S, Grible, Jacqueline M, Valentine, Aaron, Olex, Amy L, Murthy, Kavita, Chakraborty, Abhijit, Reyna, Joaquin, Figueroa, Daniela Salgado, Hinojosa-Gonzalez, Laura, Da-Inn Lee, Erika, Baur, Brittany A, Roy, Sushmita, Ay, Ferhat, Harrell, J Chuck
Published in Scientific reports (03.04.2023)
Published in Scientific reports (03.04.2023)
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Publisher Correction: Rewiring of the 3D genome during acquisition of carboplatin resistance in a triple-negative breast cancer patient-derived xenograft
Dozmorov, Mikhail G, Marshall, Maggie A, Rashid, Narmeen S, Grible, Jacqueline M, Valentine, Aaron, Olex, Amy L, Murthy, Kavita, Chakraborty, Abhijit, Reyna, Joaquin, Figueroa, Daniela Salgado, Hinojosa-Gonzalez, Laura, Da-Inn Lee, Erika, Baur, Brittany A, Roy, Sushmita, Ay, Ferhat, Harrell, J Chuck
Published in Scientific reports (09.05.2023)
Published in Scientific reports (09.05.2023)
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Author Correction: Fine mapping spatiotemporal mechanisms of genetic variants underlying cardiac traits and disease
D'Antonio, Matteo, Nguyen, Jennifer P, Arthur, Timothy D, Matsui, Hiroko, D'Antonio-Chronowska, Agnieszka, Frazer, Kelly A
Published in Nature communications (20.07.2023)
Published in Nature communications (20.07.2023)
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Abstract P1-13-23: Carboplatin resistance-associated changes in the 3D chromatin landscape of a triple-negative breast cancer Patient-Derived Xenograft
Dozmorov, Mikhail, Marshall, Maggie, Rashid, Narmeen, Grible, Jacqueline, Valentine, Aaron D., Olex, Amy, Murthy, Kavita, Chakraborty, Abhijit, Reyna, Joaquin, Figueroa, Daniela Salgado, Lee, Da-Inn, Baur, Brittany, Roy, Sushmita, Ay, Ferhat, Harrell, Chuck
Published in Cancer research (Chicago, Ill.) (01.03.2023)
Published in Cancer research (Chicago, Ill.) (01.03.2023)
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A multi-omics systems vaccinology resource to develop and test computational models of immunity
Shinde, Pramod, Soldevila, Ferran, Reyna, Joaquin, Aoki, Minori, Rasmussen, Mikkel, Willemsen, Lisa, Kojima, Mari, Ha, Brendan, Greenbaum, Jason A., Overton, James A., Guzman-Orozco, Hector, Nili, Somayeh, Orfield, Shelby, Gygi, Jeremy P., da Silva Antunes, Ricardo, Sette, Alessandro, Grant, Barry, Olsen, Lars Rønn, Konstorum, Anna, Guan, Leying, Ay, Ferhat, Kleinstein, Steven H., Peters, Bjoern
Published in Cell reports methods (25.03.2024)
Published in Cell reports methods (25.03.2024)
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Loop Catalog: a comprehensive HiChIP database of human and mouse samples
Reyna, Joaquin, Fetter, Kyra, Ignacio, Romeo, Marandi, Cemil Can Ali, Rao, Nikhil, Jiang, Zichen, Figueroa, Daniela Salgado, Bhattacharyya, Sourya, Ay, Ferhat
Published in bioRxiv : the preprint server for biology (29.04.2024)
Published in bioRxiv : the preprint server for biology (29.04.2024)
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Journal Article
A systems vaccinology resource to develop and test computational models of immunity
Shinde, Pramod, Soldevila, Ferran, Reyna, Joaquin, Aoki, Minori, Rasmussen, Mikkel, Willemsen, Lisa, Kojima, Mari, Ha, Brendan, Greenbaum, Jason A, Overton, James A, Guzman-Orozco, Hector, Nili, Somayeh, Orfield, Shelby, Gygi, Jeremy P, da Silva Antunes, Ricardo, Sette, Alessandro, Grant, Barry, Olsen, Lars Rønn, Konstorum, Anna, Guan, Leying, Ay, Ferhat, Kleinstein, Steven H, Peters, Bjoern
Published in bioRxiv : the preprint server for biology (29.08.2023)
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Published in bioRxiv : the preprint server for biology (29.08.2023)
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Putting computational models of immunity to the test - an invited challenge to predict B. pertussis vaccination outcomes
Shinde, Pramod, Willemsen, Lisa, Anderson, Michael, Aoki, Minori, Basu, Saonli, Burel, Julie G, Cheng, Peng, Dastidar, Souradipto Ghosh, Dunleavy, Aidan, Einav, Tal, schmiedt, Jamie, Fourati, Slim, Garcia, Javier, Gibson, William, Greenbaum, Jason A, Guan, Leying, Guan, Weikang, Gygi, Jeremy P, Ha, Brendan, Hou, Joe, Hsiao, Jason, Huang, Yunda, Jansen, Rick, Kakoty, Bhargob, Kang, Zhiyu, Kobie, James J, Kojima, Mari, Konstorum, Anna, Lee, Jiyeun, Lewis, Sloan A, Li, Aixin, Lock, Eric F, Mahita, Jarjapu, Mendes, Marcus, Meng, Hailong, Neher, Aidan, Nili, Somayeh, Olsen, Lars Rønn, Orfield, Shelby, Overton, James A, Pai, Nidhi, Parker, Cokie, Qian, Brian, Rasmussen, Mikkel, Reyna, Joaquin, Richardson, Eve, Safo, Sandra, Sorenson, Josey, Srinivasan, Aparna, Thrupp, Nicky, Tippalagama, Rashmi, Trevizani, Raphael, Ventz, Steffen, Wang, Jiuzhou, Wu, Cheng-Chang, Ay, Ferhat, Grant, Barry, Kleinstein, Steven H, Peters, Bjoern
Published in bioRxiv (08.09.2024)
Published in bioRxiv (08.09.2024)
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From program synthesis to optimal program synthesis
Reyna, J
Published in 2011 Annual Meeting of the North American Fuzzy Information Processing Society (01.03.2011)
Published in 2011 Annual Meeting of the North American Fuzzy Information Processing Society (01.03.2011)
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Conference Proceeding
Systematic genetic analysis of the MHC region reveals mechanistic underpinnings of HLA type associations with disease
D'antonio, Matteo, Reyna, Joaquin, Jakubosky, David, Margaret Kr Donovan, Marc-Jan Bonder, Matsui, Hiroko, Stegle, Oliver, Nariai, Naoki, D'antonio-Chronowska, Agnieszka, Frazer, Kelly A
Published in bioRxiv (15.11.2019)
Published in bioRxiv (15.11.2019)
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