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Journal Articles
- 2024
[j54]Fengyuan Huang, Robert S. Welner, Jake Y. Chen, Zongliang Yue
:
PAGER-scFGA: unveiling cell functions and molecular mechanisms in cell trajectories through single-cell functional genomics analysis. Frontiers Bioinform. 4 (2024)- [j53]Da Yan, Catia Pesquita, Carsten Görg, Jake Y. Chen:
Guest Editorial Selected Papers From BIOKDD 2022. IEEE ACM Trans. Comput. Biol. Bioinform. 21(5): 1165-1167 (2024) - 2022
- [j52]Thanh Nguyen, Zongliang Yue, Radomir Slominski, Robert S. Welner, Jianyi Zhang, Jake Y. Chen:
WINNER: A network biology tool for biomolecular characterization and prioritization. Frontiers Big Data 5 (2022) - [j51]Da Yan, Hong Qin, Hsiang-Yun Wu, Jake Y. Chen:
Guest Editorial for Selected Papers From BIOKDD 2020. IEEE ACM Trans. Comput. Biol. Bioinform. 19(5): 2545-2546 (2022) - [j50]Da Yan, Zhaohui S. Qin, Debswapna Bhattacharya, Jake Y. Chen:
Guest Editorial for Selected Papers From BIOKDD 2021. IEEE ACM Trans. Comput. Biol. Bioinform. 19(6): 3068-3069 (2022) - 2021
- [j49]Thanh Nguyen, Samuel Bharti, Zongliang Yue, Christopher D. Willey, Jake Y. Chen:
Statistical Enrichment Analysis of Samples: A General-Purpose Tool to Annotate Metadata Neighborhoods of Biological Samples. Frontiers Big Data 4: 725276 (2021) - [j48]Da Yan, Hong Qin, Hsiang-Yun Wu, Jake Y. Chen:
Editorial: AI-Enabled Data Science for COVID-19. Frontiers Big Data 4: 802452 (2021) - [j47]Thanh Nguyen, Samuel Bharti, Zongliang Yue, Christopher D. Willey, Jake Y. Chen:
Corrigendum: Statistical Enrichment Analysis of Samples: A General-Purpose Tool to Annotate Metadata Neighborhoods of Biological Samples. Frontiers Big Data 4: 804141 (2021) - [j46]Jun Deng, Thomas Hartung, Enrico Capobianco, Jake Y. Chen, Frank Emmert-Streib:
Editorial: Artificial Intelligence for Precision Medicine. Frontiers Artif. Intell. 4: 834645 (2021) - [j45]Thanh Minh Nguyen, Jacob John Jeevan, Nuo Xu, Jake Y. Chen:
Polar Gini Curve: A Technique to Discover Gene Expression Spatial Patterns from Single-cell RNA-seq Data. Genom. Proteom. Bioinform. 19(3): 493-503 (2021) - [j44]Thanh Nguyen, Tongbin Zhang, Geoffrey Fox, Sisi Zeng, Ni Cao, Chuandi Pan, Jake Y. Chen:
Linking clinotypes to phenotypes and genotypes from laboratory test results in comprehensive physical exams. BMC Medical Informatics Decis. Mak. 21-S(3): 51 (2021) - [j43]Zongliang Yue, Eric Zhang, Clark Xu, Sunny Khurana, Nishant Batra, Son Do Hai Dang, James J. Cimino, Jake Y. Chen:
PAGER-CoV: a comprehensive collection of pathways, annotated gene-lists and gene signatures for coronavirus disease studies. Nucleic Acids Res. 49(Database-Issue): D589-D599 (2021) - [j42]Guimu Guo, Hongzhi Chen, Da Yan, James Cheng, Jake Y. Chen, Zechen Chong:
Scalable De Novo Genome Assembly Using a Pregel-Like Graph-Parallel System. IEEE ACM Trans. Comput. Biol. Bioinform. 18(2): 731-744 (2021) - [j41]Da Yan, Sharma V. Thankachan, Jake Y. Chen:
Guest Editorial for Selected Papers From BIOKDD 2019. IEEE ACM Trans. Comput. Biol. Bioinform. 18(3): 809-810 (2021) - 2020
- [j40]Da Yan, Xin Gao, Samah J. Fodeh, Jake Y. Chen:
Guest Editorial for Selected Papers from BIOKDD 2018 and DMBIH 2018. IEEE ACM Trans. Comput. Biol. Bioinform. 17(6): 1832-1834 (2020) - 2019
- [j39]Zaixiang Tang, Shufeng Lei, Xinyan Zhang, Zixuan Yi, Boyi Guo, Jake Y. Chen, Yueping Shen, Nengjun Yi:
Gsslasso Cox: a Bayesian hierarchical model for predicting survival and detecting associated genes by incorporating pathway information. BMC Bioinform. 20(1): 94:1-94:15 (2019) - [j38]Zongliang Yue, Christopher D. Willey, Anita B. Hjelmeland, Jake Y. Chen:
BEERE: a web server for biomedical entity expansion, ranking and explorations. Nucleic Acids Res. 47(Webserver-Issue): W578-W586 (2019) - [j37]Zongliang Yue, Thanh Nguyen, Eric Zhang, Jianyi Zhang, Jake Y. Chen:
WIPER: Weighted in-Path Edge Ranking for biomolecular association networks. Quant. Biol. 7(4): 313-326 (2019) - 2018
- [j36]Zongliang Yue, Qi Zheng, Michael T. Neylon, Minjae Yoo, Jimin Shin, Zhiying Zhao, Aik Choon Tan, Jake Y. Chen:
PAGER 2.0: an update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology. Nucleic Acids Res. 46(Database-Issue): D668-D676 (2018) - [j35]Xin Gao, Jake Y. Chen, Mohammed J. Zaki:
Multiscale and Multimodal Analysis for Computational Biology. IEEE ACM Trans. Comput. Biol. Bioinform. 15(6): 1951-1952 (2018) - [j34]Zongliang Yue, Michael T. Neylon, Thanh Nguyen, Timothy Ratliff, Jake Y. Chen:
"Super Gene Set" Causal Relationship Discovery from Functional Genomics Data. IEEE ACM Trans. Comput. Biol. Bioinform. 15(6): 1991-1998 (2018) - 2017
- [j33]Zongliang Yue, Itika Arora, Eric Y. Zhang, Vincent Laufer, S. Louis Bridges, Jake Y. Chen:
Repositioning drugs by targeting network modules: a Parkinson's disease case study. BMC Bioinform. 18(14): 17-30 (2017) - 2015
- [j32]Zongliang Yue, Madhura M. Kshirsagar, Thanh Nguyen, Chayaporn Suphavilai, Michael T. Neylon, Liugen Zhu, Timothy Ratliff, Jake Yue Chen:
PAGER: constructing PAGs and new PAG-PAG relationships for network biology. Bioinform. 31(12): 250-257 (2015) - [j31]Hui Huang, Thanh Nguyen, Sara Ibrahim, Sandeep Shantharam, Zongliang Yue, Jake Y. Chen:
DMAP: a connectivity map database to enable identification of novel drug repositioning candidates. BMC Bioinform. 16(S13): S4 (2015) - [j30]Sarath Chandra Janga, Dongxiao Zhu, Jake Y. Chen, Mohammed J. Zaki:
Knowledge Discovery Using Big Data in Biomedical Systems. IEEE ACM Trans. Comput. Biol. Bioinform. 12(4): 726-728 (2015) - 2014
- [j29]Zongliang Yue, Ping Wan, Hui Huang, Zhan Xie, Jake Yue Chen:
SLDR: a computational technique to identify novel genetic regulatory relationships. BMC Bioinform. 15(S-11): S1 (2014) - [j28]Tianxiao Huan, Xiaogang Wu, Zengliang Bai, Jake Y. Chen:
Seed-weighted random walk ranking for cancer biomarker prioritisation: a case study in leukaemia. Int. J. Data Min. Bioinform. 9(2): 135-148 (2014) - 2013
- [j27]Huajun Chen, Tong Yu, Jake Y. Chen:
Semantic Web meets Integrative Biology: a survey. Briefings Bioinform. 14(1): 109-125 (2013) - 2012
- [j26]Hui Huang, Xiaogang Wu, Madhankumar Sonachalam, Sammed N. Mandape, Ragini Pandey, Karl F. MacDorman, Ping Wan, Jake Y. Chen:
PAGED: a pathway and gene-set enrichment database to enable molecular phenotype discoveries. BMC Bioinform. 13(S-15): S2 (2012) - [j25]Xiaogang Wu, Hui Huang, Madhankumar Sonachalam, Sina Reinhard, Jeffrey Shen, Ragini Pandey, Jake Y. Chen:
Reordering based integrative expression profiling for microarray classification. BMC Bioinform. 13(S-2): S1 (2012) - [j24]Paul J. Hale, Alfredo M. López-Yunez, Jake Y. Chen:
Genome-wide meta-analysis of genetic susceptible genes for Type 2 Diabetes. BMC Syst. Biol. 6(S-3): S16 (2012) - [j23]Xiaogang Wu, Hui Huang, Tao Wei, Ragini Pandey, Christoph Reinhard, Shuyu D. Li, Jake Y. Chen:
Network Expansion and Pathway Enrichment Analysis towards Biologically Significant Findings from Microarrays. J. Integr. Bioinform. 9(2) (2012) - [j22]Mohammad Al Hasan, Jun Huan, Jake Yue Chen, Mohammed J. Zaki:
Biological knowledge discovery and data mining. Sci. Program. 20(1): 1-2 (2012) - 2011
- [j21]Fan Zhang, Jake Y. Chen:
HOMER: a human organ-specific molecular electronic repository. BMC Bioinform. 12(S-10): S4 (2011) - [j20]Fengjun Li, Xukai Zou, Peng Liu, Jake Y. Chen:
New threats to health data privacy. BMC Bioinform. 12(S-12): S7 (2011) - [j19]Jiliang Li, Fan Zhang, Jake Y. Chen:
An integrated proteomics analysis of bone tissues in response to mechanical stimulation. BMC Syst. Biol. 5(S-3): S7 (2011) - [j18]Ping Wan, Jun Wu, Yuan Zhou, Junshu Xiao, Jie Feng, Weizhong Zhao, Shen Xiang, Guanglong Jiang, Jake Y. Chen:
Computational Analysis of Drought Stress-Associated miRNAs and miRNA Co-Regulation Network in Physcomitrella patens. Genom. Proteom. Bioinform. 9(1-2): 37-44 (2011) - 2010
- [j17]Mingyi Wang, Jake Y. Chen:
A GMM-IG framework for selecting genes as expression panel biomarkers. Artif. Intell. Medicine 48(2-3): 75-82 (2010) - [j16]Ao Zhou, Fan Zhang, Jake Y. Chen:
PEPPI: a peptidomic database of human protein isoforms for proteomics experiments. BMC Bioinform. 11(S-6): S7 (2010) - [j15]Jiao Li, Xiaoyan Zhu, Jake Yue Chen:
Discovering breast cancer drug candidates from biomedical literature. Int. J. Data Min. Bioinform. 4(3): 241-255 (2010) - [j14]Qian You, Shiaofen Fang, Jake Yue Chen:
GeneTerrain: Visual exploration of differential gene expression profiles organized in native biomolecular interaction networks. Inf. Vis. 9(1): 1-12 (2010) - [j13]Stefano Lonardi, Jake Yue Chen:
Data Mining in Bioinformatics: Selected Papers from BIOKDD. IEEE ACM Trans. Comput. Biol. Bioinform. 7(2): 195-196 (2010) - 2009
- [j12]Huajun Chen, Li Ding, Zhaohui Wu, Tong Yu, Lavanya Dhanapalan, Jake Yue Chen:
Semantic web for integrated network analysis in biomedicine. Briefings Bioinform. 10(2): 177-192 (2009) - [j11]Sudhir R. Chowbina, Xiaogang Wu, Fan Zhang, Peter M. Li, Ragini Pandey, Harini N. Kasamsetty, Jake Y. Chen:
HPD: an online integrated human pathway database enabling systems biology studies. BMC Bioinform. 10(S-11): 5 (2009) - [j10]Xiaogang Wu, Tianxiao Huan, Ragini Pandey, Tianshou Zhou, Jake Y. Chen:
Finding fractal patterns in molecular interaction networks: a case study in Alzheimer's disease. Int. J. Comput. Biol. Drug Des. 2(4): 340-352 (2009) - [j9]Jiao Li, Xiaoyan Zhu, Jake Yue Chen:
Building Disease-Specific Drug-Protein Connectivity Maps from Molecular Interaction Networks and PubMed Abstracts. PLoS Comput. Biol. 5(7) (2009) - 2008
- [j8]Tianxiao Huan, Andrey Y. Sivachenko, Scott H. Harrison, Jake Yue Chen:
ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining. BMC Bioinform. 9(S-9) (2008) - [j7]Jake Y. Chen, Mohammed Javeed Zaki, Stefano Lonardi:
BIOKDD 2008: a workshop report on data mining in bioinformatics. SIGKDD Explor. 10(2): 51-53 (2008) - 2007
- [j6]Lavanya Dhanapalan, Jake Yue Chen:
A case study of integrating protein interaction data using semantic web technology. Int. J. Bioinform. Res. Appl. 3(3): 286-302 (2007) - [j5]Jake Yue Chen, Zhong Yan, Changyu Shen, Dawn P. G. Fitzpatrick, Mu Wang:
A Systems Biology Approach to the Study of cisplatin Drug Resistance in Ovarian cancers. J. Bioinform. Comput. Biol. 5(2a): 383-405 (2007) - [j4]Megan Sickmeier, Justin A. Hamilton, Tanguy LeGall, Vladimir Vacic, Marc S. Cortese, Ágnes Tantos, Beáta Szabó, Peter Tompa, Jake Yue Chen, Vladimir N. Uversky, Zoran Obradovic, A. Keith Dunker:
DisProt: the Database of Disordered Proteins. Nucleic Acids Res. 35(Database-Issue): 786-793 (2007) - 2005
- [j3]Susie Stephens, Jake Yue Chen, Marcel G. Davidson, Shiby Thomas, Barry M. Trute:
Oracle Database 10g: a platform for BLAST search and Regular Expression pattern matching in life sciences. Nucleic Acids Res. 33(Database-Issue): 675-679 (2005) - 2004
- [j2]Susie Stephens, Jake Yue Chen, Shiby Thomas:
ODM BLAST: Sequence Homology Search in the RDBMS. IEEE Data Eng. Bull. 27(3): 20-23 (2004) - 2003
- [j1]Jake Yue Chen, John V. Carlis:
Genomic data modeling. Inf. Syst. 28(4): 287-310 (2003)
Conference and Workshop Papers
- 2024
- [c37]Da Yan, Ahmed Abdeen Hamed, Jake Y. Chen, Mohammed J. Zaki:
23rd International Workshop on Data Mining in Bioinformatics (BIOKDD 2024). KDD 2024: 6747-6748 - 2023
- [c36]Selina Zhang, Jake Yue Chen:
Designing Helicobacter pylori as an Anticancer Bacterial Vector. BCB 2023: 69:1 - [c35]Emmy Yang, Jake Y. Chen:
Accurate Identification of Human Emotional States from Images Using Deep Learning. BHI 2023: 1-4 - [c34]Da Yan, Ariful Azad, Jie Hou, Jake Y. Chen, Mohammed J. Zaki:
22nd International Workshop on Data Mining in Bioinformatics (BIOKDD 2023). KDD 2023: 5897-5898 - [c33]Huimin Xu, Chitrank Gupta, Zhandos Sembay, Swathi Thaker, Pamela Payne-Foster, Jake Y. Chen, Ying Ding:
Cross-Team Collaboration and Diversity in the Bridge2AI Project. WWW (Companion Volume) 2023: 790-794 - 2022
- [c32]Landon Dyken, Pravin Poudel, Will Usher, Steve Petruzza, Jake Y. Chen, Sidharth Kumar:
GraphWaGu: GPU Powered Large Scale Graph Layout Computation and Rendering for the Web. EGPGV@EuroVis 2022: 73-83 - [c31]Da Yan, Catia Pesquita, Carsten Görg, Jake Y. Chen, Mohammed J. Zaki:
21th International Workshop on Data Mining in Bioinformatics (BIOKDD 2022). KDD 2022: 4910-4911 - 2021
- [c30]Zongliang Yue, Nishant Batra, Hui-Chen Hsu, John Mountz, Jake Y. Chen:
PAGER-CoV-Run: An online interactive analytical platform for COVID-19 functional genomic downstream analysis. AMIA 2021 - [c29]Da Yan, Steve Qin, Debswapna Bhattacharya, Jake Y. Chen, Mohammed J. Zaki:
20th International Workshop on Data Mining in Bioinformatics (BIOKDD 2021). KDD 2021: 4175-4176 - 2020
- [c28]James J. Cimino, Wayne H. Liang, Jelai Wang, Dongmei Sun, John David Osborne, Amy Y. Wang, S. Louis Bridges, Matthew C. Wyatt, Jake Y. Chen:
Empowering Team Science Across the Translational Spectrum with the UAB Biomedical Research Infrastructure Technology Enhancement (U-BRITE). IRI 2020: 194-200 - 2016
- [c27]Jake Y. Chen, Zongliang Yue, Michael T. Neylon, Thanh Nguyen, Nafisa Bulsara, Itika Arora, Timothy Ratliff:
Towards constructing "Super Gene Sets" regulatory networks. BIBM 2016: 294-298 - [c26]Sangwoo Kim, Jake Y. Chen, Vincenzo Cutello, Doheon Lee:
DTMBIO 2016: The Tenth International Workshop on Data and Text Mining in Biomedical Informatics. CIKM 2016: 2511-2512 - 2015
- [c25]Ni Cao, Sisi Zeng, Feixia Shen, Chuandi Pan, Chengshui Chen, Thanh Nguyen, Jake Yue Chen:
Predictive and preventive models for diabetes prevention using clinical information in electronic health record. BIBM 2015: 867-874 - 2014
- [c24]Chayaporn Suphavilai, Liugen Zhu, Jake Y. Chen:
Constructing regulatory gene set networks to reveal novel insights into biological systems. ICCABS 2014: 1-2 - [c23]Zongliang Yue, Ping Wan, Zhan Xie, Jake Y. Chen:
Computational Identification of De-Centric Genetic Regulatory Relationships from Functional Genomic Data. ISBRA 2014: 224-235 - 2012
- [c22]David Johnson, Brandon Shafer, Jaehwan John Lee, Jake Y. Chen:
Multi-biomarker panel selection on a GPU. EIT 2012: 1-6 - [c21]Xiaogang Wu, Jake Y. Chen:
An evaluation for merging signaling pathways by using protein-protein interaction data. GENSiPS 2012: 203-206 - 2011
- [c20]Liang-Chin Huang, Jake Yue Chen:
A Network Biology Approach to Predicting Drug Cardiotoxicity. BIBM 2011: 278-281 - [c19]Hui Huang, Xiaogang Wu, Sara Ibrahim, Marianne McKenzie, Jake Y. Chen:
Predicting drug efficacy based on the integrated breast cancer pathway model. GENSiPS 2011: 42-45 - [c18]Xukai Zou, Peng Liu, Jake Y. Chen:
Personal genome privacy protection with feature-based hierarchical dual-stage encryption. GENSiPS 2011: 178-181 - 2010
- [c17]Fan Zhang, Mu Wang, Jake Y. Chen:
Breast cancer plasma protein biomarker discovery by coupling LC-MS/MS proteomics and systems biology. BCB 2010: 463-465 - 2009
- [c16]Jieun Jeong, Jake Y. Chen:
RIC: Ranking with Interaction Chains and Its Application in Computational Clinical Proteomics Studies. BIBM 2009: 216-221 - [c15]Fan Zhang, Jake Y. Chen:
A neural network approach to multi-biomarker panel development based on LC/MS/MS proteomics profiles: A case study in breast cancer. CBMS 2009: 1-6 - [c14]John A. Springer, Jake Y. Chen:
Toward Ontology-Driven Omics Data Integration in Current Database Management Systems. NBiS 2009: 292-297 - [c13]Qian You, Shiaofen Fang, Snehasis Mukhopadhyay, Harsha Gopal Goud Vaka, Jake Yue Chen:
Visualizing a Correlative Multi-level Graph of Biology Entity Interactions. NBiS 2009: 304-309 - [c12]Jiao Li, Pamela Crowell, Jake Yue Chen:
Construct anticancer drug-drug correlation network. SAC 2009: 771-775 - 2008
- [c11]Mingyi Wang, Jake Y. Chen:
Gene Selection using the GMM-IG Framework based Integrative Analysis. BMEI (1) 2008: 292-296 - [c10]Jiao Li, Xiaoyan Zhu, Jake Yue Chen:
Mining disease-specific molecular association profiles from biomedical literature: a case study. SAC 2008: 1287-1291 - [c9]Harini N. Kasamsetty, Xiaogang Wu, Jake Yue Chen:
Towards an integrative human pathway database for systems biology applications. SAC 2008: 1297-1301 - 2006
- [c8]Jake Yue Chen, Changyu Shen, Andrey Y. Sivachenko:
Mining Alzheimer Disease Relevant Proteins from Integrated Protein Interactome Data. Pacific Symposium on Biocomputing 2006: 367-378 - [c7]Jake Yue Chen, Sarah L. Pinkerton, Changyu Shen, Mu Wang:
An integrated computational proteomics method to extract protein targets for Fanconi Anemia studies. SAC 2006: 173-179 - 2005
- [c6]Changyu Shen, Lang Li, Jake Yue Chen:
Discover True Association Rates in Multi-protein Complex Proteomics Data Sets. CSB 2005: 167-174 - [c5]Jake Yue Chen, John V. Carlis, Ning Gao:
A complex biological database querying method. SAC 2005: 110-114 - 2004
- [c4]Jake Yue Chen, Andrey Y. Sivachenko, Lang Li:
High-throughput Protein Interactome Data: Minable or Not? BIOKDD 2004: 18-23 - [c3]Warren T. Jones, Mathew J. Palakal, Jake Yue Chen:
Editorial message: special track on bioinformatics. SAC 2004: 101 - 2003
- [c2]Jake Yue Chen, Andrey Y. Sivachenko, Russell Bell, Cornelia Kurschner, Irene Ota, Sudhir Sahasrabudhe:
Initial Large-scale Exploration of Protein-protein Interactions in Human Brain. CSB 2003: 229-234 - [c1]Jake Yue Chen, John V. Carlis:
Similar_Join: Extending DBMS with a Bio-specific Operator. SAC 2003: 109-114
Parts in Books or Collections
- 2014
- [p3]Fan Zhang, Xiaogang Wu, Jake Yue Chen:
Computational Biomarker Discovery. Approaches in Integrative Bioinformatics 2014: 355-386 - 2011
- [p2]Jake Y. Chen, Heng Xu, Pan Shi, Adam Culbertson, Eric M. Meslin:
Ethics and Privacy Considerations for Systems Biology Applications in Predictive and Personalized Medicine. Handbook of Research on Computational and Systems Biology 2011: 1-27 - 2009
- [p1]Jake Y. Chen, Shailaja Taduri, Frank Lloyd:
Design of an Online Physician-Mediated Personal Health Record System. Biomedical Data and Applications 2009: 265-279
Editorship
- 2015
- [e4]Jake Yue Chen, Mohammed J. Zaki, Tamer Kahveci, Saeed Salem, Mehmet Koyutürk:
Proceedings of the Eighth International C* Conference on Computer Science & Software Engineering, Yokohama, Japan, July 13-15, 2015. ACM 2015, ISBN 978-1-4503-3419-8 [contents] - 2013
- [e3]Gaurav Pandey, Huzefa Rangwala, George Karypis, Jake Yue Chen, Mohammed Javeed Zaki:
Proceedings of the 12th International Workshop on Data Mining in Bioinformatics, BioKDD 2013, Chicago, IL, USA, August 11, 2013. ACM 2013, ISBN 978-1-4503-2327-7 [contents] - 2012
- [e2]Tamer Kahveci, Saeed Salem, Mehmet Koyutürk, Jake Yue Chen, Mohammed J. Zaki:
Proceedings of the 11th International Workshop on Data Mining in Bioinformatics, BIOKDD 2012, Beijing, China, August 12, 2012. ACM 2012, ISBN 978-1-4503-1552-4 [contents] - 2011
- [e1]Mohammed J. Zaki, Jake Yue Chen, Mohammad Al Hasan, Jun Huan:
Proceedings of the Tenth International Workshop on Data Mining in Bioinformatics, BIOKDD '11, San Diego, California, USA, August 21, 2011. ACM 2011, ISBN 978-1-4503-0839-7 [contents]
Coauthor Index
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