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2025 Journal Article A novel paradigm for single-cell annotation in stem cell researchAtkeson, Trevor, Wilson, Sean B., Ruiz-Morales, Elias R., Little, Melissa H., Vento-Tormo, Roser, Neavin, Drew and Powell, Joseph E. (2025). A novel paradigm for single-cell annotation in stem cell research. Stem Cell Reports, 20 (12) 102707, 1-20. doi: 10.1016/j.stemcr.2025.102707 |
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2025 Journal Article Optimized summary-statistic-based single-cell eQTL meta-analysisKorshevniuk, Maryna, Westra, Harm-Jan, Oelen, Roy, van der Wijst, Monique G. P., Franke, Lude, Bonder, Marc Jan, Bonder, Marc Jan, Powell, Joseph E., Melé, Marta, Mahfouz, Ahmed, Hemberg, Martin, Ye, Jimmie, Yazar, Seyhan, Trynka, Gosia, Shin, Jay W., Shahin, Tala, Rajagopalan, Deepa, Park, Woong-Yang, Stegle, Oliver, Okada, Yukinori, Nawijn, Martijn C., Moody, Jonathan, Manikanda, Vinu, Idaghdour, Youssef, Hon, Chung-Chau, van der Harst, Pim, Groot, Hilde E., Gordon, M. Grace, Dieng, Mame M. ... Alquicira-Hernández, José (sc-eQTLGen Consortium group member) (2025). Optimized summary-statistic-based single-cell eQTL meta-analysis. Scientific Reports, 15 (1) 28407, 1. doi: 10.1038/s41598-025-08808-3 |
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2025 Journal Article Protein translation dysregulation and immune cell evasion mediated by IFN and immunoproteasome downregulation define metastatic clones in HPV-related cancer of the oropharynxChin, Venessa T., Muskovic, Walter, McCloy, Rachael A., Neavin, Drew R., Alquicira-Hernandez, Jose, Arora, Himanshi, Senabouth, Anne, Sudhakar, Kavitha Krishna, Keith, Patricia, Spenceley, Eleanor, Kaczorowski, Dominik, Floros, Peter, Leavers, Brett, Crawford, Julia A., Gallagher, Richard and Powell, Joseph E. (2025). Protein translation dysregulation and immune cell evasion mediated by IFN and immunoproteasome downregulation define metastatic clones in HPV-related cancer of the oropharynx. BMC Medicine, 23 (1) 559, 1-20. doi: 10.1186/s12916-025-04392-5 |
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2024 Journal Article Integrating population genetics, stem cell biology and cellular genomics to study complex human diseasesFarbehi, Nona, Neavin, Drew R., Cuomo, Anna S. E., Studer, Lorenz, MacArthur, Daniel G. and Powell, Joseph E. (2024). Integrating population genetics, stem cell biology and cellular genomics to study complex human diseases. Nature Genetics, 56 (5), 758-766. doi: 10.1038/s41588-024-01731-9 |
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2024 Journal Article Molecular profiling of human substantia nigra identifies diverse neuron types associated with vulnerability in Parkinson’s diseaseWang, Qian, Wang, Minghui, Choi, Insup, Sarrafha, Lily, Liang, Marianna, Ho, Lap, Farrell, Kurt, Beaumont, Kristin G., Sebra, Robert, De Sanctis, Claudia, Crary, John F., Ahfeldt, Tim, Blanchard, Joel, Neavin, Drew, Powell, Joseph, Davis, David A., Sun, Xiaoyan, Zhang, Bin and Yue, Zhenyu (2024). Molecular profiling of human substantia nigra identifies diverse neuron types associated with vulnerability in Parkinson’s disease. Science Advances, 10 (2) eadi8287, 1-18. doi: 10.1126/sciadv.adi8287 |
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2023 Journal Article Novel human pluripotent stem cell-derived hypothalamus organoids demonstrate cellular diversitySarrafha, Lily, Neavin, Drew R., Parfitt, Gustavo M., Kruglikov, Ilya A., Whitney, Kristen, Reyes, Ricardo, Coccia, Elena, Kareva, Tatyana, Goldman, Camille, Tipon, Regine, Croft, Gist, Crary, John F., Powell, Joseph E., Blanchard, Joel and Ahfeldt, Tim (2023). Novel human pluripotent stem cell-derived hypothalamus organoids demonstrate cellular diversity. iScience, 26 (9) 107525, 1-26. doi: 10.1016/j.isci.2023.107525 |
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2023 Journal Article A village in a dish model system for population-scale hiPSC studiesNeavin, Drew R., Steinmann, Angela M., Farbehi, Nona, Chiu, Han Sheng, Daniszewski, Maciej S., Arora, Himanshi, Bermudez, Yasmin, Moutinho, Cátia, Chan, Chia-Ling, Bax, Monique, Tyebally, Mubarika, Gnanasambandapillai, Vikkitharan, Lam, Chuan E., Nguyen, Uyen, Hernández, Damián, Lidgerwood, Grace E., Graham, Robert M., Hewitt, Alex W., Pébay, Alice, Palpant, Nathan J. and Powell, Joseph E. (2023). A village in a dish model system for population-scale hiPSC studies. Nature Communications, 14 (1) 3240, 1-12. doi: 10.1038/s41467-023-38704-1 |
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2023 Journal Article Pitfalls and opportunities for applying latent variables in single-cell eQTL analysesXue, Angli, Yazar, Seyhan, Neavin, Drew and Powell, Joseph E. (2023). Pitfalls and opportunities for applying latent variables in single-cell eQTL analyses. Genome Biology, 24 (1) 33, 1-11. doi: 10.1186/s13059-023-02873-5 |
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2022 Journal Article Transcriptomic and proteomic retinal pigment epithelium signatures of age-related macular degenerationSenabouth, Anne, Daniszewski, Maciej, Lidgerwood, Grace E., Liang, Helena H., Hernández, Damián, Mirzaei, Mehdi, Keenan, Stacey N., Zhang, Ran, Han, Xikun, Neavin, Drew, Rooney, Louise, Lopez Sanchez, Maria Isabel G., Gulluyan, Lerna, Paulo, Joao A., Clarke, Linda, Kearns, Lisa S., Gnanasambandapillai, Vikkitharan, Chan, Chia-Ling, Nguyen, Uyen, Steinmann, Angela M., McCloy, Rachael A., Farbehi, Nona, Gupta, Vivek K., Mackey, David A., Bylsma, Guy, Verma, Nitin, MacGregor, Stuart, Watt, Matthew J., Guymer, Robyn H. ... Pébay, Alice (2022). Transcriptomic and proteomic retinal pigment epithelium signatures of age-related macular degeneration. Nature Communications, 13 (1) 4233, 4233-1. doi: 10.1038/s41467-022-31707-4 |
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2022 Journal Article Shared genetic susceptibility between trigger finger and carpal tunnel syndrome: a genome-wide association studyPatel, Benjamin, Kleeman, Sam O, Neavin, Drew, Powell, Joseph, Baskozos, Georgios, Ng, Michael, Ahmed, Waheed-Ul-Rahman, Bennett, David L, Schmid, Annina B, Furniss, Dominic and Wiberg, Akira (2022). Shared genetic susceptibility between trigger finger and carpal tunnel syndrome: a genome-wide association study. The Lancet Rheumatology, 4 (8), e556-e565. doi: 10.1016/S2665-9913(22)00180-1 |
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2021 Journal Article ERICH3: vesicular association and antidepressant treatment responseLiu, Duan, Zhuang, Yongxian, Zhang, Lingxin, Gao, Huanyao, Neavin, Drew, Carrillo-Roa, Tania, Wang, Yani, Yu, Jia, Qin, Sisi, Kim, Daniel C., Liu, Erica, Nguyen, Thanh Thanh Le, Biernacka, Joanna M., Kaddurah-Daouk, Rima, Dunlop, Boadie W., Craighead, W. Edward, Mayberg, Helen S., Binder, Elisabeth B., Frye, Mark A., Wang, Liewei and Weinshilboum, Richard M. (2021). ERICH3: vesicular association and antidepressant treatment response. Molecular Psychiatry, 26 (6), 2415-2428. doi: 10.1038/s41380-020-00940-y |
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2021 Journal Article Single cell eQTL analysis identifies cell type-specific genetic control of gene expression in fibroblasts and reprogrammed induced pluripotent stem cellsNeavin, Drew, Nguyen, Quan, Daniszewski, Maciej S., Liang, Helena H., Chiu, Han Sheng, Wee, Yong Kiat, Senabouth, Anne, Lukowski, Samuel W., Crombie, Duncan E., Lidgerwood, Grace E., Hernández, Damián, Vickers, James C., Cook, Anthony L., Palpant, Nathan J., Pébay, Alice, Hewitt, Alex W. and Powell, Joseph E. (2021). Single cell eQTL analysis identifies cell type-specific genetic control of gene expression in fibroblasts and reprogrammed induced pluripotent stem cells. Genome Biology, 22 (1) 76, 1-19. doi: 10.1186/s13059-021-02293-3 |
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2021 Journal Article Alterations in acylcarnitines, amines, and lipids inform about the mechanism of action of citalopram/escitalopram in major depressionMahmoudianDehkordi, Siamak, Ahmed, Ahmed T., Bhattacharyya, Sudeepa, Han, Xianlin, Baillie, Rebecca A., Arnold, Matthias, Skime, Michelle K., John-Williams, Lisa St., Moseley, M. Arthur, Thompson, J. Will, Louie, Gregory, Riva-Posse, Patricio, Craighead, W. Edward, McDonald, William, Krishnan, Ranga, Rush, A. John, Frye, Mark A., Dunlop, Boadie W., Weinshilboum, Richard M., Kaddurah-Daouk, Rima, Kaddurah-Daouk, Rima, Rush, John, Tenenbaum, Jessica, Moseley, Arthur, Thompson, Will, Louie, Gregory, Blach, Colette, Mahmoudiandehkhordi, Siamak, Baillie, Rebecca ... Krishnan, Ranga (2021). Alterations in acylcarnitines, amines, and lipids inform about the mechanism of action of citalopram/escitalopram in major depression. Translational Psychiatry, 11 (1) 153, 1-14. doi: 10.1038/s41398-020-01097-6 |
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2021 Journal Article Prediction of short-term antidepressant response using probabilistic graphical models with replication across multiple drugs and treatment settingsAthreya, Arjun P., Brückl, Tanja, Binder, Elisabeth B., John Rush, A., Biernacka, Joanna, Frye, Mark A., Neavin, Drew, Skime, Michelle, Monrad, Ditlev, Iyer, Ravishankar K., Mayes, Taryn, Trivedi, Madhukar, Carter, Rickey E., Wang, Liewei, Weinshilboum, Richard M., Croarkin, Paul E. and Bobo, William V. (2021). Prediction of short-term antidepressant response using probabilistic graphical models with replication across multiple drugs and treatment settings. Neuropsychopharmacology, 46 (7), 1272-1282. doi: 10.1038/s41386-020-00943-x |
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2020 Journal Article Dual Roles for the TSPYL Family in Mediating Serotonin Transport and the Metabolism of Selective Serotonin Reuptake Inhibitors in Patients with Major Depressive DisorderQin, Sisi, Eugene, Andy R., Liu, Duan, Zhang, Lingxin, Neavin, Drew, Biernacka, Joanna M., Yu, Jia, Weinshilboum, Richard M. and Wang, Liewei (2020). Dual Roles for the TSPYL Family in Mediating Serotonin Transport and the Metabolism of Selective Serotonin Reuptake Inhibitors in Patients with Major Depressive Disorder. Clinical Pharmacology and Therapeutics, 107 (3), 662-670. doi: 10.1002/cpt.1692 |
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2020 Journal Article Acylcarnitine metabolomic profiles inform clinically-defined major depressive phenotypesAhmed, Ahmed T., MahmoudianDehkordi, Siamak, Bhattacharyya, Sudeepa, Arnold, Matthias, Liu, Duan, Neavin, Drew, Moseley, M. Arthur, Thompson, J. Will, Williams, Lisa St John, Louie, Gregory, Skime, Michelle K., Wang, Liewei, Riva-Posse, Patricio, McDonald, William M., Bobo, William V., Craighead, W. Edward, Krishnan, Ranga, Weinshilboum, Richard M., Dunlop, Boadie W., Millington, David S., Rush, A. John, Frye, Mark A. and Kaddurah-Daouk, Rima (2020). Acylcarnitine metabolomic profiles inform clinically-defined major depressive phenotypes. Journal of Affective Disorders, 264, 90-97. doi: 10.1016/j.jad.2019.11.122 |
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2019 Journal Article Pharmacogenomics-driven prediction of antidepressant treatment outcomes: a machine-learning approach with multi-trial replicationAthreya, Arjun P., Neavin, Drew, Carrillo-Roa, Tania, Skime, Michelle, Biernacka, Joanna, Frye, Mark A., Rush, A. John, Wang, Liewei, Binder, Elisabeth B., Iyer, Ravishankar K., Weinshilboum, Richard M. and Bobo, William V. (2019). Pharmacogenomics-driven prediction of antidepressant treatment outcomes: a machine-learning approach with multi-trial replication. Clinical Pharmacology and Therapeutics, 106 (4), 855-865. doi: 10.1002/cpt.1482 |
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2019 Journal Article Metabolomic signature of exposure and response to citalopram/escitalopram in depressed outpatientsBhattacharyya, Sudeepa, Ahmed, Ahmed T., Arnold, Matthias, Liu, Duan, Luo, Chunqiao, Zhu, Hongjie, Mahmoudiandehkordi, Siamak, Neavin, Drew, Louie, Gregory, Dunlop, Boadie W., Frye, Mark A., Wang, Liewei, Weinshilboum, Richard M., Krishnan, Ranga R., Rush, A. John and Kaddurah-Daouk, Rima (2019). Metabolomic signature of exposure and response to citalopram/escitalopram in depressed outpatients. Translational Psychiatry, 9 (1) 173, 1-14. doi: 10.1038/s41398-019-0507-5 |
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2019 Journal Article Pharmacogenomic next-generation DNA sequencing: Lessons from the identification and functional characterization of variants of unknown significance in CYP2C9 and CYP2C19Devarajan, Sandhya, Moon, Irene, Ho, Ming-Fen, Larson, Nicholas B., Neavin, Drew R., Moyer, Ann M., Black, John L., Bielinski, Suzette J., Scherer, Steven E., Wang, Liewei, Weinshilboum, Richard M. and Reid, Joel M. (2019). Pharmacogenomic next-generation DNA sequencing: Lessons from the identification and functional characterization of variants of unknown significance in CYP2C9 and CYP2C19. Drug Metabolism and Disposition, 47 (4), 425-435. doi: 10.1124/dmd.118.084269 |
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2018 Journal Article Beta-defensin 1, aryl hydrocarbon receptor and plasma kynurenine in major depressive disorder: Metabolomics-informed genomicsLiu, Duan, Ray, Balmiki, Neavin, Drew R., Zhang, Jiabin, Athreya, Arjun P., Biernacka, Joanna M., Bobo, William V., Hall-Flavin, Daniel K., Skime, Michelle K., Zhu, Hongjie, Jenkins, Gregory D., Batzler, Anthony, Kalari, Krishna R., Boakye-Agyeman, Felix, Matson, Wayne R., Bhasin, Swati S., Mushiroda, Taisei, Nakamura, Yusuke, Kubo, Michiaki, Iyer, Ravishankar K., Wang, Liewei, Frye, Mark A., Kaddurah-Daouk, Rima and Weinshilboum, Richard M. (2018). Beta-defensin 1, aryl hydrocarbon receptor and plasma kynurenine in major depressive disorder: Metabolomics-informed genomics. Translational Psychiatry, 8 (1) 56, 8. doi: 10.1038/s41398-017-0056-8 |
