Regulatory genomic circuitry of human disease loci by integrative epigenomics
Boix, Carles A., James, Benjamin T., Park, Yongjin P., Meuleman, Wouter, Kellis, Manolis
Published in Nature (London) (11.02.2021)
Published in Nature (London) (11.02.2021)
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Journal Article
Epigenomic dissection of Alzheimer’s disease pinpoints causal variants and reveals epigenome erosion
Xiong, Xushen, James, Benjamin T., Boix, Carles A., Park, Yongjin P., Galani, Kyriaki, Victor, Matheus B., Sun, Na, Hou, Lei, Ho, Li-Lun, Mantero, Julio, Scannail, Aine Ni, Dileep, Vishnu, Dong, Weixiu, Mathys, Hansruedi, Bennett, David A., Tsai, Li-Huei, Kellis, Manolis
Published in Cell (28.09.2023)
Published in Cell (28.09.2023)
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Journal Article
Human microglial state dynamics in Alzheimer’s disease progression
Sun, Na, Victor, Matheus B., Park, Yongjin P., Xiong, Xushen, Scannail, Aine Ni, Leary, Noelle, Prosper, Shaniah, Viswanathan, Soujanya, Luna, Xochitl, Boix, Carles A., James, Benjamin T., Tanigawa, Yosuke, Galani, Kyriaki, Mathys, Hansruedi, Jiang, Xueqiao, Ng, Ayesha P., Bennett, David A., Tsai, Li-Huei, Kellis, Manolis
Published in Cell (28.09.2023)
Published in Cell (28.09.2023)
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Journal Article
Neuronal DNA double-strand breaks lead to genome structural variations and 3D genome disruption in neurodegeneration
Dileep, Vishnu, Boix, Carles A., Mathys, Hansruedi, Marco, Asaf, Welch, Gwyneth M., Meharena, Hiruy S., Loon, Anjanet, Jeloka, Ritika, Peng, Zhuyu, Bennett, David A., Kellis, Manolis, Tsai, Li-Huei
Published in Cell (28.09.2023)
Published in Cell (28.09.2023)
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Journal Article
Single-cell atlas reveals correlates of high cognitive function, dementia, and resilience to Alzheimer’s disease pathology
Mathys, Hansruedi, Peng, Zhuyu, Boix, Carles A., Victor, Matheus B., Leary, Noelle, Babu, Sudhagar, Abdelhady, Ghada, Jiang, Xueqiao, Ng, Ayesha P., Ghafari, Kimia, Kunisky, Alexander K., Mantero, Julio, Galani, Kyriaki, Lohia, Vanshika N., Fortier, Gabrielle E., Lotfi, Yasmine, Ivey, Jason, Brown, Hannah P., Patel, Pratham R., Chakraborty, Nehal, Beaudway, Jacob I., Imhoff, Elizabeth J., Keeler, Cameron F., McChesney, Maren M., Patel, Haishal H., Patel, Sahil P., Thai, Megan T., Bennett, David A., Kellis, Manolis, Tsai, Li-Huei
Published in Cell (28.09.2023)
Published in Cell (28.09.2023)
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Journal Article
Single-cell multiregion dissection of Alzheimer’s disease
Mathys, Hansruedi, Boix, Carles A., Akay, Leyla Anne, Xia, Ziting, Davila-Velderrain, Jose, Ng, Ayesha P., Jiang, Xueqiao, Abdelhady, Ghada, Galani, Kyriaki, Mantero, Julio, Band, Neil, James, Benjamin T., Babu, Sudhagar, Galiana-Melendez, Fabiola, Louderback, Kate, Prokopenko, Dmitry, Tanzi, Rudolph E., Bennett, David A., Tsai, Li-Huei, Kellis, Manolis
Published in Nature (London) (22.08.2024)
Published in Nature (London) (22.08.2024)
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Journal Article
Neurons burdened by DNA double-strand breaks incite microglia activation through antiviral-like signaling in neurodegeneration
Welch, Gwyneth M, Boix, Carles A, Schmauch, Eloi, Davila-Velderrain, Jose, Victor, Matheus B, Dileep, Vishnu, Bozzelli, P Lorenzo, Su, Qiao, Cheng, Jemmie D, Lee, Audrey, Leary, Noelle S, Pfenning, Andreas R, Kellis, Manolis, Tsai, Li-Huei
Published in Science advances (30.09.2022)
Published in Science advances (30.09.2022)
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Journal Article
Transcriptomic and spatial dissection of human ex vivo right atrial tissue reveals proinflammatory microvascular changes in ischemic heart disease
Linna-Kuosmanen, Suvi, Schmauch, Eloi, Galani, Kyriakitsa, Ojanen, Johannes, Boix, Carles A., Örd, Tiit, Toropainen, Anu, Singha, Prosanta K., Moreau, Pierre R., Harju, Kristiina, Blazeski, Adriana, Segerstolpe, Åsa, Lahtinen, Veikko, Hou, Lei, Kang, Kai, Meibalan, Elamaran, Agudelo, Leandro Z., Kokki, Hannu, Halonen, Jari, Jalkanen, Juho, Gunn, Jarmo, MacRae, Calum A., Hollmén, Maija, Hartikainen, Juha E.K., Kaikkonen, Minna U., García-Cardeña, Guillermo, Tavi, Pasi, Kiviniemi, Tuomas, Kellis, Manolis
Published in Cell reports. Medicine (21.05.2024)
Published in Cell reports. Medicine (21.05.2024)
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Journal Article
Single-cell atlas of ABCA7 loss-of-function reveals impaired neuronal respiration via choline-dependent lipid imbalances
von Maydell, Djuna, Wright, Shannon, Bonner, Julia Maeve, Staab, Colin, Spitaleri, Andrea, Liu, Liwang, Pao, Ping-Chieh, Yu, Chung Jong, Scannail, Aine Ni, Li, Mingpei, Boix, Carles A, Mathys, Hansruedi, Leclerc, Guillaume, Menchaca, Gloria Suella, Welch, Gwyneth, Graziosi, Agnese, Leary, Noelle, Samaan, George, Kellis, Manolis, Tsai, Li-Huei
Published in bioRxiv (28.06.2024)
Published in bioRxiv (28.06.2024)
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Journal Article
Multi‐polygenic score model informs the genetic basis of heterogeneity in Alzheimer’s disease
Tanigawa, Yosuke, Sun, Na, Li, William F, Boix, Carles A, Galani, Kyriaki, Mathys, Hansruedi, Bennett, David A. A, Tsai, Li‐Huei, Kellis, Manolis
Published in Alzheimer's & dementia (01.12.2023)
Published in Alzheimer's & dementia (01.12.2023)
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Journal Article
Deep learning modeling of ribosome profiling reveals regulatory underpinnings of translatome and interprets disease variants
He, Jialin, Xiong, Lei, Shi, Shaohui, Li, Chengyu, Chen, Kexuan, Fang, Qianchen, Jiuhong Nan, Ding, Ke, Li, Jingyun, Mao, Yuanhui, Boix, Carles A, Hu, Xinyang, Kellis, Manolis, Xiong, Xushen
Published in bioRxiv (01.03.2024)
Published in bioRxiv (01.03.2024)
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Paper
Single-cell mosaicism analysis reveals cell-type-specific somatic mutational burden in Alzheimer's Dementia
Kousi, Maria, Boix, Carles A, Park, Yongjin P, Mathys, Hansruedi, Sledzieski, Samuel, Peng, Zhuyu, Bennett, David A, Li-Huei Tsai, Kellis, Manolis
Published in bioRxiv (22.04.2022)
Published in bioRxiv (22.04.2022)
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Paper
Cardiovascular disease causes proinflammatory microvascular changes in the human right atrium
Linna-Kuosmanen, Suvi, Schmauch, Eloi, Galani, Kyriakitsa, Ojanen, Johannes, Boix, Carles A, Örd, Tiit, Toropainen, Anu, Singha, Prosanta K, Moreau, Pierre R, Harju, Kristiina, Blazeski, Adriana, Segerstolpe, Asa, Lahtinen, Veikko, Hou, Lei, Kang, Kai, Meibalan, Elamaran, Agudelo, Leandro Z, Kokki, Hannu, Halonen, Jari, Jalkanen, Juho, Gunn, Jarmo, Macrae, Calum A, Hollmen, Maija, Hartikainen, Juha, Kaikkonen, Minna U, Garcia-Cardena, Guillermo, Tavi, Pasi, Kiviniemi, Tuomas, Kellis, Manolis
Published in bioRxiv (27.12.2022)
Published in bioRxiv (27.12.2022)
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Paper
The ENCODE Imputation Challenge: A critical assessment of methods for cross-cell type imputation of epigenomic profiles
Schreiber, Jacob Matthew, Boix, Carles A, Lee, Jin Wook, Li, Hongyang, Guan, Yuanfang, Chang, Chun-Chieh, Jen-Chien, Chang, Hawkins-Hooker, Alex, Schoelkopf, Bernhard, Schweikert, Gabriele, Mateo Rojas Carulla, Canakoglu, Arif, Guzzo, Francesco, Nanni, Luca, Masseroli, Marco, Carman, Mark James, Pinoli, Pietro, Hong, Chenyang, Yip, Kevin Y, Spence, Jeffrey P, Sanjit Singh Batra, Song, Yun S, Mahony, Shaun, Zhang, Zheng, Tan, Wuwei, Shen, Yang, Sun, Yuanfei, Shi, Minyi, Jessika Adrian, Sandstrom, Richard S, Farrell, Nina, Halow, Jessica M, Lee, Kristen, Jiang, Lixia, Yang, Xinqiong, Epstein, Charles B, Strattan, J Seth, Snyder, Michael P, Kellis, Manolis, Noble, William S, Kundaje, Anshul Bharat
Published in bioRxiv (02.08.2022)
Published in bioRxiv (02.08.2022)
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