TDP-43 and other hnRNPs regulate cryptic exon inclusion of a key ALS/FTD risk gene, UNC13A
Koike, Yuka, Pickles, Sarah, Estades Ayuso, Virginia, Jansen-West, Karen, Qi, Yue A, Li, Ziyi, Daughrity, Lillian M, Yue, Mei, Zhang, Yong-Jie, Cook, Casey N, Dickson, Dennis W, Ward, Michael, Petrucelli, Leonard, Prudencio, Mercedes
Published in PLoS biology (17.03.2023)
Published in PLoS biology (17.03.2023)
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Identification of neoepitope reactive T-cell receptors guided by HLA-A03:01 and HLA-A11:01 immunopeptidomics
Ade, Catherine M, Sporn, Matthew J, Das, Sudipto, Yu, Zhiya, Hanada, Ken-ichi, Qi, Yue A, Maity, Tapan, Zhang, Xu, Guha, Udayan, Andresson, Thorkell, Yang, James C
Published in Journal for immunotherapy of cancer (01.09.2023)
Published in Journal for immunotherapy of cancer (01.09.2023)
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Alterations in HLA Class I-Presented Immunopeptidome and Class I-Interactome upon Osimertinib Resistance in EGFR Mutant Lung Adenocarcinoma
Qi, Yue A., Maity, Tapan K., Gao, Shaojian, Gong, Tao, Bahta, Meriam, Venugopalan, Abhilash, Zhang, Xu, Guha, Udayan
Published in Cancers (04.10.2021)
Published in Cancers (04.10.2021)
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Variant biomarker discovery using mass spectrometry-based proteogenomics
Reilly, Luke, Seddighi, Sahba, Singleton, Andrew B, Cookson, Mark R, Ward, Michael E, Qi, Yue A
Published in Frontiers in aging (24.04.2023)
Published in Frontiers in aging (24.04.2023)
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A fully automated FAIMS-DIA mass spectrometry-based proteomic pipeline
Reilly, Luke, Lara, Erika, Ramos, Daniel, Li, Ziyi, Pantazis, Caroline B., Stadler, Julia, Santiana, Marianita, Roberts, Jessica, Faghri, Faraz, Hao, Ying, Nalls, Mike A., Narayan, Priyanka, Liu, Yansheng, Singleton, Andrew B., Cookson, Mark R., Ward, Michael E., Qi, Yue A.
Published in Cell reports methods (23.10.2023)
Published in Cell reports methods (23.10.2023)
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Application of Aligned-UMAP to longitudinal biomedical studies
Dadu, Anant, Satone, Vipul K., Kaur, Rachneet, Koretsky, Mathew J., Iwaki, Hirotaka, Qi, Yue A., Ramos, Daniel M., Avants, Brian, Hesterman, Jacob, Gunn, Roger, Cookson, Mark R., Ward, Michael E., Singleton, Andrew B., Campbell, Roy H., Nalls, Mike A., Faghri, Faraz
Published in Patterns (New York, N.Y.) (09.06.2023)
Published in Patterns (New York, N.Y.) (09.06.2023)
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Profiling the Skeletal Muscle Proteome in Patients on Atypical Antipsychotics and Mood Stabilizers
Burghardt, Kyle J, Calme, Griffin, Caruso, Michael, Howlett, Bradley H, Sanders, Elani, Msallaty, Zaher, Mallisho, Abdullah, Seyoum, Berhane, Qi, Yue A, Zhang, Xiangmin, Yi, Zhengping
Published in Brain sciences (12.02.2022)
Published in Brain sciences (12.02.2022)
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TDP-43 loss and ALS-risk SNPs drive mis-splicing and depletion of UNC13A
Brown, Anna-Leigh, Wilkins, Oscar G, Keuss, Matthew J, Hill, Sarah E, Zanovello, Matteo, Lee, Weaverly Colleen, Bampton, Alexander, Lee, Flora C Y, Masino, Laura, Qi, Yue A, Bryce-Smith, Sam, Gatt, Ariana, Hallegger, Martina, Fagegaltier, Delphine, Phatnani, Hemali, Newcombe, Jia, Gustavsson, Emil K, Seddighi, Sahba, Reyes, Joel F, Coon, Steven L, Ramos, Daniel, Schiavo, Giampietro, Fisher, Elizabeth M C, Raj, Towfique, Secrier, Maria, Lashley, Tammaryn, Ule, Jernej, Buratti, Emanuele, Humphrey, Jack, Ward, Michael E, Fratta, Pietro
Published in Nature (London) (03.03.2022)
Published in Nature (London) (03.03.2022)
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The short-chain fatty acid acetate coordinates with CD30 to modulate T-cell survival
Lyu, Junfang, Li, Ziyi, Roberts, Jessica P, Qi, Yue A, Xiong, Jianhua
Published in Molecular biology of the cell (01.07.2023)
Published in Molecular biology of the cell (01.07.2023)
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A cellular taxonomy of the adult human spinal cord
Yadav, Archana, Matson, Kaya J.E., Li, Li, Hua, Isabelle, Petrescu, Joana, Kang, Kristy, Alkaslasi, Mor R., Lee, Dylan I., Hasan, Saadia, Galuta, Ahmad, Dedek, Annemarie, Ameri, Sara, Parnell, Jessica, Alshardan, Mohammad M., Qumqumji, Feras Abbas, Alhamad, Saud M., Wang, Alick Pingbei, Poulen, Gaetan, Lonjon, Nicolas, Vachiery-Lahaye, Florence, Gaur, Pallavi, Nalls, Mike A., Qi, Yue A., Maric, Dragan, Ward, Michael E., Hildebrand, Michael E., Mery, Pierre-Francois, Bourinet, Emmanuel, Bauchet, Luc, Tsai, Eve C., Phatnani, Hemali, Le Pichon, Claire E., Menon, Vilas, Levine, Ariel J.
Published in Neuron (Cambridge, Mass.) (01.02.2023)
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Proteogenomic Analysis Unveils the HLA Class I-Presented Immunopeptidome in Melanoma and EGFR-Mutant Lung Adenocarcinoma
Qi, Yue A., Maity, Tapan K., Cultraro, Constance M., Misra, Vikram, Zhang, Xu, Ade, Catherine, Gao, Shaojian, Milewski, David, Nguyen, Khoa D., Ebrahimabadi, Mohammad H., Hanada, Ken-ichi, Khan, Javed, Sahinalp, Cenk, Yang, James C., Guha, Udayan
Published in Molecular & cellular proteomics (01.01.2021)
Published in Molecular & cellular proteomics (01.01.2021)
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Correction: TDP-43 and other hnRNPs regulate cryptic exon inclusion of a key ALS/FTD risk gene, UNC13A
Koike, Yuka, Pickles, Sarah, Ayuso, Virginia Estades, Jansen-West, Karen, Qi, Yue A, Li, Ziyi, Daughrity, Lillian M, Yue, Mei, Zhang, Yong-Jie, Cook, Casey N, Dickson, Dennis W, Ward, Michael, Petrucelli, Leonard, Prudencio, Mercedes
Published in PLoS biology (14.07.2023)
Published in PLoS biology (14.07.2023)
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Mis-spliced transcripts generate de novo proteins in TDP-43-related ALS/FTD
Seddighi, Sahba, Qi, Yue A, Brown, Anna-Leigh, Wilkins, Oscar G, Bereda, Colleen, Belair, Cedric, Zhang, Yong-Jie, Prudencio, Mercedes, Keuss, Matthew J, Khandeshi, Aditya, Pickles, Sarah, Kargbo-Hill, Sarah E, Hawrot, James, Ramos, Daniel M, Yuan, Hebao, Roberts, Jessica, Sacramento, Erika Kelmer, Shah, Syed I, Nalls, Mike A, Colón-Mercado, Jennifer M, Reyes, Joel F, Ryan, Veronica H, Nelson, Matthew P, Cook, Casey N, Li, Ziyi, Screven, Laurel, Kwan, Justin Y, Mehta, Puja R, Zanovello, Matteo, Hallegger, Martina, Shantaraman, Anantharaman, Ping, Lingyan, Koike, Yuka, Oskarsson, Björn, Staff, Nathan P, Duong, Duc M, Ahmed, Aisha, Secrier, Maria, Ule, Jernej, Jacobson, Steven, Reich, Daniel S, Rohrer, Jonathan D, Malaspina, Andrea, Dickson, Dennis W, Glass, Jonathan D, Ori, Alessandro, Seyfried, Nicholas T, Maragkakis, Manolis, Petrucelli, Leonard, Fratta, Pietro, Ward, Michael E
Published in Science translational medicine (14.02.2024)
Published in Science translational medicine (14.02.2024)
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TMEM106B core deposition associates with TDP-43 pathology and is increased in risk SNP carriers for frontotemporal dementia
Marks, Jordan D, Ayuso, Virginia Estades, Carlomagno, Yari, Yue, Mei, Todd, Tiffany W, Hao, Ying, Li, Ziyi, McEachin, Zachary T, Shantaraman, Anantharaman, Duong, Duc M, Daughrity, Lillian M, Jansen-West, Karen, Shao, Wei, Calliari, Anna, Bejarano, Jesus Gonzalez, DeTure, Michael, Rawlinson, Bailey, Casey, Monica Castanedes, Lilley, Meredith T, Donahue, Megan H, Jawahar, Vidhya Maheswari, Boeve, Bradley F, Petersen, Ronald C, Knopman, David S, Oskarsson, Björn, Graff-Radford, Neill R, Wszolek, Zbigniew K, Dickson, Dennis W, Josephs, Keith A, Qi, Yue A, Seyfried, Nicholas T, Ward, Michael E, Zhang, Yong-Jie, Prudencio, Mercedes, Petrucelli, Leonard, Cook, Casey N
Published in Science translational medicine (17.01.2024)
Published in Science translational medicine (17.01.2024)
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Meeting Report on the 3rd Chinese American Society for Mass Spectrometry Conference—Advancing Biological and Pharmaceutical Mass Spectrometry
Chen, Hao, Fu, Yunlin, Han, Mei, Han, Xianlin, Hao, Ling, Huan, Tao, Huang, Lan, Huang, Ming, Ji, Qin, Jiang, Tao, Jiang, Yong, Li, Liang, Li, Lingjun, Liang, Xiaorong, Lih, Mamie, Lin, Yanping, Liu, Xiaowen, Liu, Tao, Liu, Yansheng, Ma, Shuguang, Peng, Junmin, Qi, Yue A., Qu, Jun, Shou, Wilson, Sun, Liangliang, Wang, Mingxun, Wang, Shuai, Wu, Ronghu, Wu, Si, Yan, Xin, Yang, Jun, Yang, Weiming, Yang, Zhibo, Yu, Yonghao, Zhang, Hui, Zhang, Hui, Zhao, Shouxun, Zhu, Jiangjiang, Zhu, Ying, Wang, Yinsheng, Weng, Naidong
Published in Biomedical chromatography (01.03.2024)
Published in Biomedical chromatography (01.03.2024)
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Mis-spliced transcripts generate de novo proteins in TDP-43-related ALS/FTD
Seddighi, Sahba, Qi, Yue A, Brown, Anna-Leigh, Wilkins, Oscar G, Bereda, Colleen, Belair, Cedric, Zhang, Yongjie, Prudencio, Mercedes, Keuss, Matthew J, Khandeshi, Aditya, Pickles, Sarah, Hill, Sarah E, Hawrot, James, Ramos, Daniel M, Yuan, Hebao, Roberts, Jessica, Kelmer Sacramento, Erika, Shah, Syed I, Nalls, Mike A, Colon-Mercado, Jenn, Reyes, Joel F, Ryan, Veronica H, Nelson, Matthew P, Cook, Casey, Li, Ziyi, Screven, Laurel, Kwan, Justin Y, Shantaraman, Anantharaman, Ping, Lingyan, Koike, Yuka, Oskarsson, Björn, Staff, Nathan, Duong, Duc M, Ahmed, Aisha, Secrier, Maria, Ule, Jerneg, Jacobson, Steven, Rohrer, Jonathan, Malaspina, Andrea, Glass, Jonathan D, Ori, Alessandro, Seyfried, Nicholas T, Maragkakis, Manolis, Petrucelli, Leonard, Fratta, Pietro, Ward, Michael E
Published in bioRxiv (23.01.2023)
Published in bioRxiv (23.01.2023)
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A reference human induced pluripotent stem cell line for large-scale collaborative studies
Pantazis, Caroline B., Yang, Andrian, Lara, Erika, McDonough, Justin A., Blauwendraat, Cornelis, Peng, Lirong, Oguro, Hideyuki, Kanaujiya, Jitendra, Zou, Jizhong, Sebesta, David, Pratt, Gretchen, Cross, Erin, Blockwick, Jeffrey, Buxton, Philip, Kinner-Bibeau, Lauren, Medura, Constance, Tompkins, Christopher, Hughes, Stephen, Santiana, Marianita, Faghri, Faraz, Nalls, Mike A., Vitale, Daniel, Ballard, Shannon, Qi, Yue A., Ramos, Daniel M., Anderson, Kailyn M., Stadler, Julia, Narayan, Priyanka, Papademetriou, Jason, Reilly, Luke, Nelson, Matthew P., Aggarwal, Sanya, Rosen, Leah U., Kirwan, Peter, Pisupati, Venkat, Coon, Steven L., Scholz, Sonja W., Priebe, Theresa, Öttl, Miriam, Dong, Jian, Meijer, Marieke, Janssen, Lara J.M., Lourenco, Vanessa S., van der Kant, Rik, Crusius, Dennis, Paquet, Dominik, Raulin, Ana-Caroline, Bu, Guojun, Held, Aaron, Wainger, Brian J., Gabriele, Rebecca M.C., Casey, Jackie M., Wray, Selina, Abu-Bonsrah, Dad, Parish, Clare L., Beccari, Melinda S., Cleveland, Don W., Li, Emmy, Rose, Indigo V.L., Kampmann, Martin, Calatayud Aristoy, Carles, Verstreken, Patrik, Heinrich, Laurin, Chen, Max Y., Schüle, Birgitt, Dou, Dan, Holzbaur, Erika L.F., Zanellati, Maria Clara, Basundra, Richa, Deshmukh, Mohanish, Cohen, Sarah, Khanna, Richa, Raman, Malavika, Nevin, Zachary S., Matia, Madeline, Van Lent, Jonas, Timmerman, Vincent, Conklin, Bruce R., Johnson Chase, Katherine, Zhang, Ke, Funes, Salome, Bosco, Daryl A., Erlebach, Lena, Welzer, Marc, Kronenberg-Versteeg, Deborah, Lyu, Guochang, Arenas, Ernest, Coccia, Elena, Sarrafha, Lily, Ahfeldt, Tim, Marioni, John C., Skarnes, William C., Cookson, Mark R., Ward, Michael E., Merkle, Florian T.
Published in Cell stem cell (01.12.2022)
Published in Cell stem cell (01.12.2022)
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Abstract 273: A mass spectrometry survey of frequent HLA alleles successfully presenting common tumor specific mutations for immune recognition
Ade, Catherine M., Qi, Yue A., Das, Sudipto, Hanada, Ken-ichi, Maity, Tapan, Zhang, Xu, Andresson, Thorkell, Guha, Udayan, Yang, James C.
Published in Cancer research (Chicago, Ill.) (01.07.2021)
Published in Cancer research (Chicago, Ill.) (01.07.2021)
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Common ALS/FTD risk variants in UNC13A exacerbate its cryptic splicing and loss upon TDP-43 mislocalization
Brown, Anna-Leigh, Wilkins, Oscar G, Keuss, Matthew J, Hill, Sarah E, Zanovello, Matteo, Weaverly, Colleen Lee, Lee, Flora Cy, Masino, Laura, Qi, Yue A, Bryce-Smith, Sam, Bampton, Alexander, Gatt, Ariana, Phatnani, Hemali, Nygc Als Consortium, Schiavo, Giampietro, Elizabeth Mc Fisher, Towfique Raj, Secrier, Maria, Lashley, Tammaryn, Ule, Jernej, Buratti, Emanuele, Humphrey, Jack, Ward, Michael E, Fratta, Pietro
Published in bioRxiv (04.04.2021)
Published in bioRxiv (04.04.2021)
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Author Correction: TDP-43 loss and ALS-risk SNPs drive mis-splicing and depletion of UNC13A
Brown, Anna-Leigh, Wilkins, Oscar G., Keuss, Matthew J., Hill, Sarah E., Zanovello, Matteo, Lee, Weaverly Colleen, Bampton, Alexander, Lee, Flora C. Y., Masino, Laura, Qi, Yue A., Bryce-Smith, Sam, Gatt, Ariana, Hallegger, Martina, Fagegaltier, Delphine, Phatnani, Hemali, Kwan, Justin, Sareen, Dhruv, Broach, James R., Simmons, Zachary, Arcila-Londono, Ximena, Lee, Edward B., Van Deerlin, Vivianna M., Shneider, Neil A., Fraenkel, Ernest, Ostrow, Lyle W., Baas, Frank, Zaitlen, Noah, Berry, James D., Malaspina, Andrea, Fratta, Pietro, Cox, Gregory A., Thompson, Leslie M., Finkbeiner, Steve, Dardiotis, Efthimios, Miller, Timothy M., Chandran, Siddharthan, Pal, Suvankar, Hornstein, Eran, MacGowan, Daniel J., Heiman-Patterson, Terry, Hammell, Molly G., Patsopoulos, Nikolaos. A., Butovsky, Oleg, Dubnau, Joshua, Nath, Avindra, Bowser, Robert, Harms, Matthew, Aronica, Eleonora, Poss, Mary, Phillips-Cremins, Jennifer, Crary, John, Atassi, Nazem, Lange, Dale J., Adams, Darius J., Stefanis, Leonidas, Gotkine, Marc, Baloh, Robert H., Babu, Suma, Raj, Towfique, Paganoni, Sabrina, Shalem, Ophir, Smith, Colin, Zhang, Bin, Harris, Brent, Broce, Iris, Drory, Vivian, Ravits, John, McMillan, Corey, Menon, Vilas, Wu, Lani, Altschuler, Steven, Lerner, Yossef, Sattler, Rita, Van Keuren-Jensen, Kendall, Rozenblatt-Rosen, Orit, Lindblad-Toh, Kerstin, Nicholson, Katharine, Gregersen, Peter, Lee, Jeong-Ho, Koks, Sulev, Muljo, Stephen, Newcombe, Jia, Gustavsson, Emil K., Seddighi, Sahba, Reyes, Joel F., Coon, Steven L., Ramos, Daniel, Schiavo, Giampietro, Fisher, Elizabeth M. C., Raj, Towfique, Secrier, Maria, Lashley, Tammaryn, Ule, Jernej, Buratti, Emanuele, Humphrey, Jack, Ward, Michael E., Fratta, Pietro
Published in Nature (London) (11.07.2024)
Published in Nature (London) (11.07.2024)
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