Multiomic QTL mapping reveals phenotypic complexity of GWAS loci and prioritizes putative causal variants

Authors: Arias, Angelo D., Benaglio, Paola, Berggren, W. Travis, Borja, Victor, Cook, Megan, DeBoever, Christopher, Diffenderfer, Kenneth E., Donovan, Margaret K.R., Farnam, KathyJean, Fujita, Kyohei, Garcia, Melvin, Harismendy, Olivier, Jakubosky, David, Jepsen, Kristen, Joshua, Isaac, Li, He, Matsui, Hiroko, McCarron, Angelina, Nariai, Naoki, O’Connor, Daniel T., Okubo, Jonathan, Rao, Fengwen, Reyna, Joaquin, Aguiar, Lana Ribeiro, Salgado, Bianca M., Silva, Nayara, Smith, Erin N., Sohmer, Josh, Yost, Shawn, Young Greenwald, William W., Arthur, Timothy D. ^{1, 2, 11}, Nguyen, Jennifer P. ^{2, 3, 11}, Henson, Benjamin A. ⁴, D'Antonio-Chronowska, Agnieszka ⁵, Jaureguy, Jeffrey ^{3, 6}, Panopoulos, Athanasia D. ^{8, 9}, Izpisua Belmonte, Juan Carlos ¹⁰, D’Antonio, Matteo ², McVicker, Graham ⁶, Frazer, Kelly A. ^{4, 7, 12, ∗}

Source: In Cell Genomics 12 March 2025 5(3)

iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types

Authors: 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.

Source: In Stem Cell Reports 11 April 2017 8(4):1086-1100

Complex regulatory networks influence pluripotent cell state transitions in human iPSCs.

Authors: Arthur, Timothy D., Nguyen, Jennifer P., D'Antonio-Chronowska, Agnieszka, Matsui, Hiroko, Silva, Nayara S., Joshua, Isaac N., iPSCORE Consortium, Aguiar, Lana Ribeiro, Arias, Angelo D., Benaglio, Paola, Berggren, W. Travis, Belmonte, Juan Carlos Izpisua, Borja, Victor, Cook, Megan, DeBoever, Christopher, Diffenderfer, Kenneth E., Donovan, Margaret K. R., Farnam, KathyJean, Fujita, Kyohei, Garcia, Melvin

Source: Nature Communications; 2/23/2024, Vol. 15 Issue 1, p1-19, 19p

Subject Terms: BINDING sites, STEM cells, TRANSCRIPTION factors, GENE regulatory networks, GENE expression, HUMAN beings

Fine mapping spatiotemporal mechanisms of genetic variants underlying cardiac traits and disease.

Authors: D'Antonio, Matteo, Nguyen, Jennifer P., Arthur, Timothy D., Arias, Angelo D., Benaglio, Paola, Berggren, W. Travis, Borja, Victor, Belmonte, Juan Carlos Izpisua, Cook, Megan, DeBoever, Christopher, Diffenderfer, Kenneth E., Donovan, Margaret K. R., Farnam, KathyJean, Frazer, Kelly A., Fujita, Kyohei, Garcia, Melvin, Harismendy, Olivier, Henson, Benjamin A., Jakubosky, David, Jepsen, Kristen

Source: Nature Communications; 7/21/2023, Vol. 14 Issue 1, p1-18, 18p

Subject Terms: GENETIC variation, LOCUS (Genetics), GENE expression, ATRIAL fibrillation, GENOME-wide association studies

Dynamic regulation of CTCF stability and sub-nuclear localization in response to stress.

Authors: Lehman, Bettina J.¹, Lopez-Diaz, Fernando J.¹, Santisakultarm, Thom P.², Fang, Linjing², Shokhirev, Maxim N.³, Diffenderfer, Kenneth E.⁴, Manor, Uri², Emerson, Beverly M.¹, emersobe@ohsu.edu

Source: PLoS Genetics; 1/7/2021, Vol. 17 Issue 1, p1-34, 34p

Aberrant DNA Methylation in Human iPSCs Associates with MYC-Binding Motifs in a Clone-Specific Manner Independent of Genetics

Authors: Panopoulos, Athanasia D., Smith, Erin N., Arias, Angelo D., Shepard, Peter J., Hishida, Yuriko, Modesto, Veronica, Diffenderfer, Kenneth E., Conner, Clay, Biggs, William, Sandoval, Efren, D’Antonio-Chronowska, Agnieszka, Berggren, W. Travis, Izpisua Belmonte, Juan Carlos, Frazer, Kelly A.

Source: Cell stem cell. 20(4):505-517.e6

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100052461645.0x000001&indx=1&recIds=ETOCvdc_100052461645.0x000001

The San Diego Nathan Shock Center: tackling the heterogeneity of aging.

Authors: Shadel, Gerald S., Adams, Peter D., Berggren, W. Travis, Diedrich, Jolene K., Diffenderfer, Kenneth E., Gage, Fred H., Hah, Nasun, Hansen, Malene, Hetzer, Martin W., Molina, Anthony J. A., Manor, Uri, Marek, Kurt, O'Keefe, David D., Pinto, Antonio F. M., Sacco, Alessandra, Sharpee, Tatyana O., Shokriev, Maxim N., Zambetti, Stefania

Source: GeroScience; Oct2021, Vol. 43 Issue 5, p2139-2148, 10p

Subject Terms: AGING, MENTORING, CELLULAR aging, AGE, NATURE & nurture, ECOLOGICAL genetics

Importance of WNT-dependent signaling for derivation and maintenance of primed pluripotent bovine embryonic stem cells†

Authors: Xiao, Yao, Amaral, Thiago F, Ross, Pablo J, Soto, Delia A, Diffenderfer, Kenneth E, Pankonin, Aimee R, Jeensuk, Surawich, Tríbulo, Paula, Hansen, Peter J

Source: Biology of Reproduction; July 2021, Vol. 105 Issue: 1 p52-63, 12p

Differential responses to lithium in hyperexcitable neurons from patients with bipolar disorder.

Authors: Mertens, Jerome, Wang, Qiu-Wen, Kim, Yongsung, Yu, Diana X., Pham, Son, Yang, Bo, Zheng, Yi, Diffenderfer, Kenneth E., Zhang, Jian, Soltani, Sheila, Eames, Tameji, Schafer, Simon T., Boyer, Leah, Marchetto, Maria C., Nurnberger, John I., Calabrese, Joseph R., Ødegaard, Ketil J., McCarthy, Michael J., Zandi, Peter P., Alba, Martin

Source: Nature. 11/5/2015, Vol. 527 Issue 7576, p95-99. 5p. 1 Chart, 13 Graphs.

Subjects: BIPOLAR disorder, THERAPEUTIC use of lithium, NEURONS, NEUROLOGICAL disorders, PLURIPOTENT stem cells, PSYCHOLOGY

Author Correction: Fine mapping spatiotemporal mechanisms of genetic variants underlying cardiac traits and disease.

Authors: D'Antonio, Matteo, Nguyen, Jennifer P., Arthur, Timothy D., iPSCORE Consortium, Arias, Angelo D., Benaglio, Paola, Berggren, W. Travis, Borja, Victor, Belmonte, Juan Carlos Izpisua, Cook, Megan, DeBoever, Christopher, Diffenderfer, Kenneth E., Donovan, Margaret K. R., Farnam, KathyJean, Frazer, Kelly A., Fujita, Kyohei, Garcia, Melvin, Harismendy, Olivier, Henson, Benjamin A., Jakubosky, David

Source: Nature Communications; 7/20/2023, Issue 1, p1-1, 1p

Subject Terms: GENETIC variation, CONSORTIA

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Erratum: Differential responses to lithium in hyperexcitable neurons from patients with bipolar disorder.

Authors: Mertens, Jerome, Wang, Qiu-Wen, Kim, Yongsung, Yu, Diana X., Pham, Son, Yang, Bo, Zheng, Yi, Diffenderfer, Kenneth E., Zhang, Jian, Soltani, Sheila, Eames, Tameji, Schafer, Simon T., Boyer, Leah, Marchetto, Maria C., Nurnberger, John I., Calabrese, Joseph R., Oedegaard, Ketil J., McCarthy, Michael J., Zandi, Peter P., Alda, Martin

Source: Nature; 2/11/2016, Vol. 530 Issue 7589, p242-242, 1p