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9 results on '"Dong, Qilin"'

3. Prediction of amino acid side chain conformation using a deep neural network

Author

Liu, Ke, Sun, Xiangyan, Ma, Jun, Zhou, Zhenyu, Dong, Qilin, Peng, Shengwen, Wu, Junqiu, Tan, Suocheng, Blobel, Günter, and Fan, Jie

Subjects
Quantitative Biology - Biomolecules, Computer Science - Learning, Statistics - Machine Learning
Abstract

A deep neural network based architecture was constructed to predict amino acid side chain conformation with unprecedented accuracy. Amino acid side chain conformation prediction is essential for protein homology modeling and protein design. Current widely-adopted methods use physics-based energy functions to evaluate side chain conformation. Here, using a deep neural network architecture without physics-based assumptions, we have demonstrated that side chain conformation prediction accuracy can be improved by more than 25%, especially for aromatic residues compared with current standard methods. More strikingly, the prediction method presented here is robust enough to identify individual conformational outliers from high resolution structures in a protein data bank without providing its structural factors. We envisage that our amino acid side chain predictor could be used as a quality check step for future protein structure model validation and many other potential applications such as side chain assignment in Cryo-electron microscopy, crystallography model auto-building, protein folding and small molecule ligand docking.

Published
2017

4. Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease

Author

Allen, Genevera I, Amoroso, Nicola, Anghel, Catalina, Balagurusamy, Venkat, Bare, Christopher J, Beaton, Derek, Bellotti, Roberto, Bennett, David A, Boehme, Kevin L, Boutros, Paul C, Caberlotto, Laura, Caloian, Cristian, Campbell, Frederick, Neto, Elias Chaibub, Chang, Yu‐Chuan, Chen, Beibei, Chen, Chien‐Yu, Chien, Ting‐Ying, Clark, Tim, Das, Sudeshna, Davatzikos, Christos, Deng, Jieyao, Dillenberger, Donna, Dobson, Richard JB, Dong, Qilin, Doshi, Jimit, Duma, Denise, Errico, Rosangela, Erus, Guray, Everett, Evan, Fardo, David W, Friend, Stephen H, Fröhlich, Holger, Gan, Jessica, St George‐Hyslop, Peter, Ghosh, Satrajit S, Glaab, Enrico, Green, Robert C, Guan, Yuanfang, Hong, Ming‐Yi, Huang, Chao, Hwang, Jinseub, Ibrahim, Joseph, Inglese, Paolo, Iyappan, Anandhi, Jiang, Qijia, Katsumata, Yuriko, Kauwe, John SK, Klein, Arno, Kong, Dehan, Krause, Roland, Lalonde, Emilie, Lauria, Mario, Lee, Eunjee, Lin, Xihui, Liu, Zhandong, Livingstone, Julie, Logsdon, Benjamin A, Lovestone, Simon, Ma, Tsung‐wei, Malhotra, Ashutosh, Mangravite, Lara M, Maxwell, Taylor J, Merrill, Emily, Nagorski, John, Namasivayam, Aishwarya, Narayan, Manjari, Naz, Mufassra, Newhouse, Stephen J, Norman, Thea C, Nurtdinov, Ramil N, Oyang, Yen‐Jen, Pawitan, Yudi, Peng, Shengwen, Peters, Mette A, Piccolo, Stephen R, Praveen, Paurush, Priami, Corrado, Sabelnykova, Veronica Y, Senger, Philipp, Shen, Xia, Simmons, Andrew, Sotiras, Aristeidis, Stolovitzky, Gustavo, Tangaro, Sabina, Tateo, Andrea, Tung, Yi‐An, Tustison, Nicholas J, Varol, Erdem, Vradenburg, George, Weiner, Michael W, Xiao, Guanghua, Xie, Lei, Xie, Yang, Xu, Jia, Yang, Hojin, Zhan, Xiaowei, Zhou, Yunyun, Zhu, Fan, and Zhu, Hongtu

Subjects
Biomedical and Clinical Sciences, Biological Psychology, Clinical Sciences, Neurosciences, Psychology, Acquired Cognitive Impairment, Prevention, Neurodegenerative, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Dementia, Alzheimer's Disease, Aging, Brain Disorders, Neurological, Alzheimer Disease, Apolipoproteins E, Biomarkers, Cognition Disorders, Computational Biology, Databases, Bibliographic, Humans, Predictive Value of Tests, Azheimer's disease, Crowdsource, Big data, Bioinformatics, Cognitive decline, Imaging, Genetics, Alzheimer's Disease Neuroimaging Initiative, Geriatrics, Clinical sciences, Biological psychology
Abstract

Identifying accurate biomarkers of cognitive decline is essential for advancing early diagnosis and prevention therapies in Alzheimer's disease. The Alzheimer's disease DREAM Challenge was designed as a computational crowdsourced project to benchmark the current state-of-the-art in predicting cognitive outcomes in Alzheimer's disease based on high dimensional, publicly available genetic and structural imaging data. This meta-analysis failed to identify a meaningful predictor developed from either data modality, suggesting that alternate approaches should be considered for prediction of cognitive performance.

Published
2016

6. Topology optimization design of optical bench for airborne electro-optical platform

Author

Zhu Lei, Yan Weiliang, Huizhen Li, Liu Hu, Zhang Lanlan, Hou Rui, Dong Qilin, and Jia Zhaohui

Subjects
Acceleration, Modal superposition, Computer science, Topology optimization, Structure (category theory), Topology (electrical circuits), Topology
Abstract

The purpose of this paper is to demonstrate a topology optimization design method of the optical bench of airborne electro-optical platform to save the structural weight and maintain the dynamic performances. The dynamic responses under random acceleration excitations are analysed using the modal superposition method. A pseudo-density based topology optimization model is then formulated to solve the problem. Further detailed design of the optical bench structure is carried out according to the optimized structural topology. Compared with the initial design, the optimized structure is improved with the total weight saved and the dynamic responses satisfied.

Published
2020

7. F1 lightning

Author

Yang, Jiacheng, primary, Rae, Ian, additional, Xu, Jun, additional, Shute, Jeff, additional, Yuan, Zhan, additional, Lau, Kelvin, additional, Zeng, Qiang, additional, Zhao, Xi, additional, Ma, Jun, additional, Chen, Ziyang, additional, Gao, Yuan, additional, Dong, Qilin, additional, Zhou, Junxiong, additional, Wood, Jeremy, additional, Graefe, Goetz, additional, Naughton, Jeff, additional, and Cieslewicz, John, additional

Published
2020
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9. Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease

Author

Luxembourg Centre for Systems Biomedicine (LCSB): Biomedical Data Science (Glaab Group) [research center], Fonds National de la Recherche - FnR [sponsor], Allen, Genevera, Amoroso, Nicola, Anghel, Catalina, Balagurusamy, Venkat, Bare, Christopher, Beaton, Derek, Bellotti, Roberto, Bennett, David, Boehme, Kevin, Caberlotto, Laura, Campbell, Frederick, Chang, Yu-Chuan, Chen, Beibei, Chen, Chien-Yu, Chien, Ting-Ying, Clark, Tim, Das, Sudeshna, Davatzikos, Christos, Deng, Jieyao, Dillenberger, Donna, Dobson, Richard, Dong, Qilin, Doshi, Jimit, Duma, Denise, Errico, Rosangela, Erus, Guray, Everett, Evan, Fardo, David, Friend, Stephen, Fröhlich, Holger, Gan, Jessica, St George-Hyslop, Peter, Ghosh, Satrajit, Glaab, Enrico, Green, Robert, Guan, Yuanfang, Hong, Ming-Yi, Huang, Chao, Hwang, Jinseub, Ibrahim, Joseph, Inglese, Paolo, Jiang, Qijia, Katsumata, Yurik, Kauwe, Jo, Klein, Arno, Kong, Dehan, Krause, Roland, Lalonde, Emilie, Lauria, Mari, Lee, Eunjee, Lin, Xihui, Liu, Zhandong, Livingstone, Julie, Logsdon, Benjami, Lovestone, Simon, Iyappan, Anandhi, Ma, Tsung-wei, Malhotra, Ashutos, Maxwell, Taylor, Merrill, Emily, Nagorski, John, Alex Namasivayam, Aishwarya, Narayan, Manjari, Naz, Mufassra, Neto, Elias Chaibub, Newhouse, Stephen, Norman, Thea, Nurtdinov, Ramil, Oyang, Yen-Jen, Boutros, Paul, Pawitan, Yudi, Peng, Shengwen, Peters, Mette, Piccolo, Stephen, Praveen, Paurush, Priami, Corrado, Sabelnykova, Veronica, Senger, Philipp, Shen, Xia, Simmons, Andrew, Sotiras, Aristeidis, Stolovitzky, Gustavo, Tangaro, Sabina, Tateo, Andrea, Tung, Yi-An, Tustison, Nicholas, Varol, Erdem, Vradenburg, George, Weiner, Michael, Xiao, Guanghua, Xie, Lei, Xie, Yang, Xu, Jia, Yang, Hojin, Zhan, Xiaowei, Zhou, Yunyun, Zhu, Fan, Zhu, Hongtu, Zhu, Shanfeng, Alzheimer's Disease Neuroimaging Initiative, Luxembourg Centre for Systems Biomedicine (LCSB): Biomedical Data Science (Glaab Group) [research center], Fonds National de la Recherche - FnR [sponsor], Allen, Genevera, Amoroso, Nicola, Anghel, Catalina, Balagurusamy, Venkat, Bare, Christopher, Beaton, Derek, Bellotti, Roberto, Bennett, David, Boehme, Kevin, Caberlotto, Laura, Campbell, Frederick, Chang, Yu-Chuan, Chen, Beibei, Chen, Chien-Yu, Chien, Ting-Ying, Clark, Tim, Das, Sudeshna, Davatzikos, Christos, Deng, Jieyao, Dillenberger, Donna, Dobson, Richard, Dong, Qilin, Doshi, Jimit, Duma, Denise, Errico, Rosangela, Erus, Guray, Everett, Evan, Fardo, David, Friend, Stephen, Fröhlich, Holger, Gan, Jessica, St George-Hyslop, Peter, Ghosh, Satrajit, Glaab, Enrico, Green, Robert, Guan, Yuanfang, Hong, Ming-Yi, Huang, Chao, Hwang, Jinseub, Ibrahim, Joseph, Inglese, Paolo, Jiang, Qijia, Katsumata, Yurik, Kauwe, Jo, Klein, Arno, Kong, Dehan, Krause, Roland, Lalonde, Emilie, Lauria, Mari, Lee, Eunjee, Lin, Xihui, Liu, Zhandong, Livingstone, Julie, Logsdon, Benjami, Lovestone, Simon, Iyappan, Anandhi, Ma, Tsung-wei, Malhotra, Ashutos, Maxwell, Taylor, Merrill, Emily, Nagorski, John, Alex Namasivayam, Aishwarya, Narayan, Manjari, Naz, Mufassra, Neto, Elias Chaibub, Newhouse, Stephen, Norman, Thea, Nurtdinov, Ramil, Oyang, Yen-Jen, Boutros, Paul, Pawitan, Yudi, Peng, Shengwen, Peters, Mette, Piccolo, Stephen, Praveen, Paurush, Priami, Corrado, Sabelnykova, Veronica, Senger, Philipp, Shen, Xia, Simmons, Andrew, Sotiras, Aristeidis, Stolovitzky, Gustavo, Tangaro, Sabina, Tateo, Andrea, Tung, Yi-An, Tustison, Nicholas, Varol, Erdem, Vradenburg, George, Weiner, Michael, Xiao, Guanghua, Xie, Lei, Xie, Yang, Xu, Jia, Yang, Hojin, Zhan, Xiaowei, Zhou, Yunyun, Zhu, Fan, Zhu, Hongtu, Zhu, Shanfeng, and Alzheimer's Disease Neuroimaging Initiative

Published
2016

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