Publications
Translational informatics is the main focus of the AI.MED lab’s research. Working on the interface between bioinformatics and clinical research, lab members work to create new techniques and databases to improve clinical care, diagnosis, treatment and to advance clinical research. Jake Chen, Ph.D., the lab’s principal investigator, has research interests in systems biology, data mining, advanced visual analytics for therapeutic discovery and clinical decision-making applications. His lab is working to build biomolecular systems models from biomedical big data in an attempt to understand, simulate and predict complex disease biology outcomes.
Andrzej T Slominski, Tae-Kang Kim, Shariq Qayyum, Yuwei Song, Zorica Janjetovic, Allen SW Oak, Radomir M Slominski, Chander Raman, Joanna Stefan, Carlos A Mier-Aguilar, Venkatram Atigadda, David K Crossman, Andriy Golub, Yaroslav Bilokin, Edith K Y Tang, Jake Y. Chen, Robert C Tuckey, Anton M Jetten, Yuhua Song (2021)
The interactions of derivatives of lumisterol (L3) and vitamin D3 (D3) with liver X receptors (LXRs) were investigated. Molecular docking using crystal structures of the ligand binding domains (LBDs) of LXRα and β revealed high docking scores for L3 and D3 hydroxymetabolites, similar to those of the natural ligands, predicting good binding to the receptor. RNA sequencing of murine dermal fibroblasts stimulated with D3-hydroxyderivatives revealed LXR as the second nuclear receptor pathway for several D3-hydroxyderivatives, including 1,25(OH)2D3. This was validated by their induction of genes downstream of LXR. L3 and D3-derivatives activated an LXR-response element (LXRE)-driven reporter in CHO cells and human keratinocytes, and by enhanced expression of LXR target genes. L3 and D3 derivatives showed high affinity binding to the LBD of the LXRα and β in LanthaScreen TR-FRET LXRα and β coactivator assays…Read More
Xiaowen Liu, PhD1,2; Zongliang Yue, MS3 ; Yimou Cao, MS1 ; Lauren Taylor, MD2 ; Qing Zhang, MS4 ; Sung W. Choi, MD5 ; Samir Hanash, MD, PhD6 ; Sawa Ito, MD7 ; Jake Y. Chen, PhD3 ; Huanmei Wu, PhD1 ; and Sophie Paczesny, MD, PhD2
As a tumor immunotherapy, allogeneic hematopoietic cell transplantation with subsequent donor lymphocyte injection (DLI) aims to induce the graft-versus-tumor (GVT) effect but often also leads to acute graftversus-host disease (GVHD). Plasma tests that can predict the likelihood of GVT without GVHD are still needed…read more
Conference or Workshop Proceedings Articles
| Number | Name | Type | Year | Researchgate | Endnote | |
|---|---|---|---|---|---|---|
| 1 | Jake Chen*, Michael Neylon, Zongliang Yue, Thanh Nguyen, Timothy Ratliff (2016) Towards Constructing “Super Gene Sets” Regulatory Networks, Proceedings of the 2016 International Conference on Bioinformatics & Biomedicine, Shenzhen, China, doi: 10.1109/BIBM.2016.7822534. | Conference or Workshop Proceedings Articles | 2016 | |||
| 2 | Ni Cao, Sisi Zeng, Feixia Shen, Chuandi Pan, Chengshui Chen, Thanh Nguen, and Jake Chen* (2015) Predictive and Preventive Models for Diabetes Prevention using Clinical Information in Electronic Health Record, Proceedings of the 2015 International Conference on Bioinformatics & Biomedicine, Washington, DC, pp. 867-874. | Conference or Workshop Proceedings Articles | 2015 | |||
| 3 | Thanh Nguyen, Junjie Chen, Dongxiang Ji, Xiaoru Sun, Chuandi Pan,* Chengshui Chen*, and Jake Y. Chen* (2015) An Integrated Machine Learning and Network Analysis to Discover Marker Clinical Measurement in Lung Cancer, Proceedings of 2015 International Conference on Genome Medicine, eds. Le L & Pham S, Ho Chi Minh City, Viet Nam. | Conference or Workshop Proceedings Articles | 2015 | |||
| 4 | Chayaporn Suphavilai, Liugen Zhu, and Jake Y. Chen* (2014) Constructing Regulatory Gene Set Network to Reveal Novel Insights into Biological Systems, Proceedings of the IEEE 4th International Conference on Computational Advances in Bio and medical Sciences, Miami Beach, FL, doi: 10.1109/ICCABS.2014.6863927. | Conference or Workshop Proceedings Articles | 2014 | |||
| 5 | Xiaogang Wu and Jake Chen* (2012) An Evaluation for Merging Signaling Pathways by Using Protein-Protein Interaction Data, Proceedings of IEEE International Workshop on Genomic Signal Processing and Statistics, Washington, DC. | Conference or Workshop Proceedings Articles | 2012 | |||
| 6 | David Johnson, Brandon Shafer, Jaehwan John Lee, and Jake Chen* (2012) Multi-Biomarker Panel Selection on a GPU, Proceedings of IEEE International Conference on Electro/Information Technology, Indianapolis, IN. | Conference or Workshop Proceedings Articles | 2012 | |||
| 7 | Xiaogang Wu, Hui Huang, Tao Wei, Ragini Pandey, Christopher Reinhard, Shuyu D. Li, Jake Y. Chen* (2012) Network Expansion and Pathway Enrichment Analysis towards Biologically Significant Findings from Microarrays, Proceedings of the Eighth Annual International Symposium on Integrative Bioinformatics, Hangfzhou, Zhejiang, China. | Conference or Workshop Proceedings Articles | 2012 | |||
| 8 | Liang-Chin Huang and Jake Y. Chen* (2011) A Network Biology Approach to Predicting Drug Cardiotoxicity, Proceedings of the International Conference on Bioinformatics & Biomedicine, Atlanta, GA, pp. 278-281. | Conference or Workshop Proceedings Articles | 2011 | |||
| 9 | Jason McLaughlin, Qian You, Shiaofen Fang, and Jake Y. Chen* (2011) TAO: Terrain Analytic Operators for Expert-Guided Data Mining Applications, Workshop on Visual Analytics in Healthcare, Providence, RI. | Conference or Workshop Proceedings Articles | 2011 | |||
| 10 | Hui Huang, Xiaogang Wu, Sara Ibrahim, Marianne Mckenzie, Sunil Badve, and Jake Y. Chen* (2011) Predicting Drug Efficacy Based on the Integrated Breast Cancer Pathway Model, 2011 IEEE International Workshop on Genomic Signal Processing and Statistics, San Antonio, TX. | Conference or Workshop Proceedings Articles | 2011 | |||
| 11 | Xiaogang Wu and Jake Y. Chen* (2011) Network Reordering Based Integrative Expression Profiling for Microarray Classification, 2011 Great Lakes Bioinformatics Conference, Athens, OH. | Conference or Workshop Proceedings Articles | 2011 | |||
| 12 | Xukai Zou*, Peng Liu*, and Jake Y. Chen* (2011) Personal Genome Privacy Protection with Feature-based Hierarchical Dual-stage Encryptions, 2011 IEEE International Workshop on Genomic Signal Processing and Statistics, San Antonio, TX. | Conference or Workshop Proceedings Articles | 2011 | |||
| 13 | Fan Zhang and Jake Y. Chen* (2010) Novel Protein Isoform Biomarker Identifications from Proteomes, 2nd International Workshop on Data Mining for Biomarker Discovery at the 2010 IEEE International Conference of Bioinformatics and Biomedicine, Hong Kong. | Conference or Workshop Proceedings Articles | 2011 | |||
| 14 | Hui Huang, Xiaogang Wu, Shuyu Li, Sara Ibrahim, Taiwo Ajumobi, and Jake Y. Chen* (2010) Evaluate Drug Effects on Gene Expression Profiles with Connectivity Maps, 2nd International Workshop on Data Mining for Biomarker Discovery at the 2010 IEEE International Conference of Bioinformatics and Biomedicine, Hong Kong. | Conference or Workshop Proceedings Articles | 2010 | |||
| 15 | Fan Zhang and Jake Y. Chen* (2010) Proteome-scale Protein Isoform Characterization with High Performance Computing, 2010 Microsoft eScience Workshop Proceedings, Berkeley, CA. | Conference or Workshop Proceedings Articles | 2010 | |||
| 16 | Fengjun Li, Jake Y. Chen, Xukai Zou, and Peng Liu (2010) New Privacy Threats in Healthcare Informatics: When Medical Records Join the Web, Ninth ACM SIGKDD Workshop on Data Mining in Bioinformatics (BioKDD 2010) at the International Conference on Knowledge Discovery and Data Mining, Washington, DC. (Acceptance rate: 37%) | Conference or Workshop Proceedings Articles | 2010 | |||
| 17 | Fan Zhang, Mu Wang, and Jake Y. Chen* (2010) Breast Cancer Plasma Protein Biomarker Discovery by Coupling LC-MS/MS Proteomics and Systems Biology, Proceedings of the ACM International Conference on Bioinformatics and Computational Biology, Niagara Falls, NY. (poster paper; accepted) | Conference or Workshop Proceedings Articles | 2010 | |||
| 18 | Tianxiao Huan, Xiaogang Wu, Zengliang Bai, and Jake Y. Chen* (2010) Random Walk Ranking Guided by Disease Association Networks for Lung Cancer Biomarker Discovery, Proceedings of the International Symposium on Biocomputing, Vol. 1, No. 33, pp. 1-8. (Acceptance rate: 30%) | Conference or Workshop Proceedings Articles | 2010 | |||
| 19 | Jieun Jeong and Jake Y. Chen* (2009) RIC: Ranking with Interaction Chains and its Applications in Computational Clinical Proteomics Studies, Proceedings of the International Conference on Bioinformatics & Biomedicine, pp. 216-221. (Acceptance rate: 17% out of 256 submissions) | Conference or Workshop Proceedings Articles | 2009 | |||
| 20 | Tianxiao Huan, Xiaogang Wu, Zengliang Bai, and Jake Y. Chen* (2009) SWRWR: Seed-weighted Random Walks Ranking Method and Its Application to Leukemia Cancer Biomarker Prioritizations, IEEE International Conference on Bioinformatics and Biomedicine Workshop 2009, pp. 220-225. (Acceptance rate: <35%) | Conference or Workshop Proceedings Articles | 2009 | |||
| 21 | Fan Zhang and Jake Y. Chen* (2009) A Neural Network Approach to Multi-biomarker Panel Development Based on LC/MS/MS Proteomics Profiles: A Case Study in Breast Cancer, Proceedings of the 22nd IEEE Symposium on Computer-Based Medical Systems, pp. 1-6, doi: 10.1109/CBMS.2009.5255456. | Conference or Workshop Proceedings Articles | 2009 | |||
| 22 | Hui Huang, Jiao Li, and Jake Y. Chen* (2009) Disease Gene-fishing in Molecular Interaction Networks: a Case Study in Colorectal Cancer, Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society, pp. 6416-6419. | Conference or Workshop Proceedings Articles | 2009 | |||
| 23 | Xiaogang Wu, Ragini Pandey, and Jake Y. Chen* (2009) Network Topological Reordering Revealing Systemic Patterns in Yeast Protein Interaction Networks, Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society, pp. 6416-6419. | Conference or Workshop Proceedings Articles | 2009 | |||
| 24 | Qian You, Shiaofen Fang, Snehasis Mukhopadhyay, Harsha Vaka, and Jake Y. Chen* (2009) Visualizing a Correlative Multi-level Graph of Biology Entity Interactions, Workshop on Intelligent Biomedical Information Systems at the 12th International Conference on Network-Based Information Systems, pp.304-309. | Conference or Workshop Proceedings Articles | 2009 | |||
| 25 | John Springer and Jake Y. Chen* (2009) Toward Ontology-Driven Omics Data Integration in Current Database Management Systems, Workshop on Intelligent Biomedical Information Systems at the 12th International Conference on Network-Based Information Systems, pp. 292-297. | Conference or Workshop Proceedings Articles | 2009 | |||
| 26 | Jiao Li, Pamela Crowell, and Jake Y. Chen* (2009) Construct Anticancer Drug-Drug Correlation Network, Proceedings of the 24th Annual ACM Symposium on Applied Computing, Vol. 2, pp. 771-775. (Acceptance rate: 28%) | Conference or Workshop Proceedings Articles | 2009 | |||
| 27 | Mingyi Wang and Jake Y. Chen* (2008) Gene Selection using the GMM-IG Framework based Integrative Analysis. IEEE Proceedings of the International Conference on Biomedical Engineering and Informatics, Vol.1, pp. 292-296. (Acceptance rate: ~30%, out of >700 submissions) | Conference or Workshop Proceedings Articles | 2008 | |||
| 28 | Harini Kasamsetty, Xiaogang Wu, and Jake Y. Chen* (2008) An Integrative Human Pathway Database for Systems Biology Applications. Proceedings of the 23rd Annual ACM Symposium on Applied Computing, pp. 1297-1301. (Acceptance rate: 24%, 9 out of 38 submissions for BIO track) | Conference or Workshop Proceedings Articles | 2008 | |||
| 29 | Jiao Li, Xiaoyan Zhu, and Jake Y. Chen* (2008) Mining Disease-Specific Molecular Association Profiles from Biomedical Literature: A Case Study. Proceedings of the 23rd Annual ACM Symposium on Applied Computing, pp. 1287-1291. (Acceptance rate: 24%, 9 out of 38 submissions for BIO track) | Conference or Workshop Proceedings Articles | 2008 | |||
| 30 | Jake Y. Chen*, Changyu Shen, Zhong Yan, Dawn P. G. Brown, and Mu Wang (2006) A Systems Biology Case Study of Ovarian Cancer Drug Resistance. Computational Systems Bioinformatics: CSB2006 Conference Proceedings, edited by Peter Markstein and Ying Xu, Series on Advances in Bioinformatics and Computational Biology, Vol. 4, pp. 389-398. (Acceptance rate: 19%, out of 154 submissions) | Conference or Workshop Proceedings Articles | 2006 | |||
| 31 | Jake Y. Chen*, Sarah L. Pinkerton, Changyu Shen, and Mu Wang (2006) An Integrated Computational Proteomics Method to Extract Protein Targets for Fanconi Anemia Studies. Proceedings of the 21st Annual ACM Symposium on Applied Computing, Dijon, France, Vol. I, pp. 173-179. (Acceptance rate: 32%) | Conference or Workshop Proceedings Articles | 2006 | |||
| 32 | Jake Y. Chen*, Changyu Shen, and Andrey Sivachenko (2006) Mining Alzheimer Disease Relevant Proteins from Integrated Protein Interactome Data. Pacific Symposium on Biocomputing, Vol. 11, pp. 367-378. (Acceptance rate: 20%) | Conference or Workshop Proceedings Articles | 2006 | |||
| 33 | Changyu Shen, Lang Li, Jake Y. Chen* (2005) Discover True Association Rates in Multi-protein Complex Proteomics Data Sets. Proceedings of the IEEE Computational Systems Biology Bioinformatics Conference, Stanford University, Stanford, CA, Vol. 1, pp. 167-174. (Acceptance rate: 12%, out of 246 submissions) | Conference or Workshop Proceedings Articles | 2005 | |||
| 34 | Jake Y. Chen*, John Carlis, and Ning Gao (2005) A Method for Conquering Complex Biological Database Queries. Proceedings of the 20th Annual ACM Symposium on Applied Computing, Santa Fe, NM, Vol. I, pp. 110-114. (Acceptance rate: 35%) | Conference or Workshop Proceedings Articles | 2005 | |||
| 35 | Jake Y. Chen* (2004) Experience with Processing and Exploration of High-throughput Protein Interaction Data, Session on Systems Biology and Bioinformatics. Proceedings of the Eighth World Multi-Conference on Systemics, Cybernetics and Informatics, Orlando, FL, Vol. VII, pp. 41-45. | Conference or Workshop Proceedings Articles | 2004 | |||
| 36 | Jake Y. Chen*, Andrey Y. Sivachenko, and Lang Li (2004) High-throughput Protein Interactome Data: Minable or Not? Fourth ACM SIGKDD Workshop on Data Mining in Bioinformatics (BioKDD 2004) at the International Conference on Knowledge Discovery and Data Mining, Seattle, WA, pp. 18-23. (Acceptance rate: 38%) | Conference or Workshop Proceedings Articles | 2004 | |||
| 37 | Jake Y. Chen*, Andrey Y. Sivachenko, Russell Bell, Connie Kurschner, Irene Ota, and Sudhir Sahasrabudhe (2003) Initial Large-scale Exploration of Protein-protein Interactions in the Human Brain. Proceedings of the IEEE CSB Bioinformatics Conference, Stanford University, Stanford, CA, published by IEEE Computer Society Press, pp. 229-234. (Acceptance rate: 18%) | Conference or Workshop Proceedings Articles | 2003 | |||
| 38 | Jake Y. Chen* and John Carlis (2003) Similar_Join: Extending DBMS with a Bio-specific Operator. Proceedings of the 18th ACM Symposium on Applied Computing, Melbourne, Florida, pp. 109-114. (Acceptance rate: 33%) | Conference or Workshop Proceedings Articles | 2003 | |||
| 39 | Jake Y. Chen* and John Carlis (2002) Managing Bioinformatics Challenges in Expression Microarray Sequence Selection Projects. Proceedings of the Second Chinese Conference on Bioinformatics, Beijing, China. | Conference or Workshop Proceedings Articles | 2002 | |||
| 40 | Jake Y. Chen* and John Carlis (2002) A High-density Microarray Case Study of Query Modeling In Bioinformatics. Proceedings of the International Conference on Bioinformatics 2002, Bangkok, Thailand. | Conference or Workshop Proceedings Articles | 2002 | |||
| 41 | Yue Chen*, Libby Shoop, John Carlis, and John Riedl (2001) A High-throughput System to Resolve Inconsistent Reading Frame Predictions for Expressed Sequence Tags. Proceedings of Workshop on Inconsistency in Data and Knowledge at the International Joint Conference on Artificial Intelligence (IJCAI), Seattle, WA. | Conference or Workshop Proceedings Articles | 2001 |
Conference Proceedings and Journal Special Issues
| Number | Name | Type | Year | Researchgate | Endnote | |
|---|---|---|---|---|---|---|
| 1 | Xin Gao, Jake Y. Chen, and Mohammed Zaki, ed. (2018) Special Issue on BIOKDD Workshop 2016, IEEE/ACM Transactions on Computational Biology and Bioinformatics. Published by IEEE press. | Edited Conference Proceedings and Journal Special Issues | 2018 | |||
| 2 | Sarath Chandra Janga, Dongxiao Zhu, Jake Y. Chen, and Mohammed J. Zaki, ed. (2015) IEEE/ACM Transactions on Computational Biology and Bioinformatics. Published by IEEE press. | Edited Conference Proceedings and Journal Special Issues | 2015 | |||
| 3 | Jake Y. Chen and Vasant Honavar, ed. (2014) Proceedings of IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences. IEEE. | Edited Conference Proceedings and Journal Special Issues | 2014 | |||
| 4 | Sarath Janga, Dongxiao Zhu, Jake Y. Chen, and Mohammed Zaki, ed. (2014) Proceedings of the Thirteenth International Workshop on Data Mining in Bioinformatics. ACM 2014. | Edited Conference Proceedings and Journal Special Issues | 2014 | |||
| 5 | Gaurav Pandey, Huzefa Rangwala, George Karypis, Jake Y. Chen, and Mohammed Zaki, ed. (2013) Proceedings of the Twelfth International Workshop on Data Mining in Bioinformatics. ACM 2013, ISBN 978-1-4503-2327-7. | Edited Conference Proceedings and Journal Special Issues | 2013 | |||
| 6 | Vincent S. Tseng, Hui-Huang Hsu, and Jake Y. Chen, ed. (2012) Special Issue on Data Mining for Biomarker Discovery, International Journal of Data Mining in Bioinformatics. | Edited Conference Proceedings and Journal Special Issues | 2012 | |||
| 7 | Tamer Kahveci, Saeed Salem, Mehmet Koyuturk, Jake Y. Chen, and Mohammed Zaki, ed. (2012) Proceedings of the Eleventh International Workshop on Data Mining in Bioinformatics. ACM 2012, ISBN 978-1-4503-1552-4. | Edited Conference Proceedings and Journal Special Issues | 2012 | |||
| 8 | Jake Y. Chen, Mohammed Zaki, Mohammad Hasan, and Jun Huan, ed. (2011) Proceedings of the Tenth International Workshop on Data Mining in Bioinformatics. Published by ACM SIGKDD. | Edited Conference Proceedings and Journal Special Issues | 2011 | |||
| 9 | Vincent S. Tseng, Hui-Huang Hsu, and Jake Y. Chen, ed. (2010) Proceedings of the Second International Workshop on Data Mining in Bioinformatics. Published by IEEE press. | Edited Conference Proceedings and Journal Special Issues | 2010 | |||
| 10 | Luke Huan, Jake Y. Chen, and Mohammed Zaki, ed. (2010) Proceedings of the Ninth International Workshop on Data Mining in Bioinformatics. Published by ACM SIGKDD. | Edited Conference Proceedings and Journal Special Issues | 2010 | |||
| 11 | Vincent S. Tseng, Hui-Huang Hsu, and Jake Y. Chen, ed. (2009) Proceedings of the International Workshop on Data Mining in Bioinformatics. 34 pages. Published by IEEE press. | Edited Conference Proceedings and Journal Special Issues | 2009 | |||
| 12 | Stefano Lonardi and Jake Y. Chen, ed. (2008) Special Issue on Data Mining in Bioinformatics (BIOKDD 2007), Journal of Bioinformatics and Computational Biology, Vol. 6, No. 6. | Edited Conference Proceedings and Journal Special Issues | 2008 | |||
| 13 | Stefano Lonardi, Jake Y. Chen, and Mohammed Zaki, ed. (2008) Proceedings of the Eighth International Workshop on Data Mining in Bioinformatics. 70 pages. Published by ACM SIGKDD. | Edited Conference Proceedings and Journal Special Issues | 2008 | |||
| 14 | Amandeep S. Sidhu, Tharam S. Dillon, Elizabeth Chang and Jake Y. Chen, ed. (2007) Special Issue on Ontologies for Bioinformatics, International Journal of Bioinformatics Research and Applications, Vol. 3, No. 3. | Edited Conference Proceedings and Journal Special Issues | 2007 | |||
| 15 | Jake Y. Chen, Stefano Lonardi, and Mohammed Zaki, ed. (2007) Proceedings of the Seventh International Workshop on Data Mining in Bioinformatics. 87 pages. Published by ACM SIGKDD. | Edited Conference Proceedings and Journal Special Issues | 2007 | |||
| 16 | Katsuhisa Horimoto, Jake Chen, and Amy Chan, ed. (2004) Applications of Informatics and Cybernetics in Science and Engineering, Proceedings of the 8th World Multi-Conference on Systemics, Cybernetics and Informatics (Vol. VII). ISBN: 980-6560-13-2. | Edited Conference Proceedings and Journal Special Issues | 2004 |
Books
| Number | Name | Researchgate | Endnote | Type | Year | |
|---|---|---|---|---|---|---|
| 1 | Jake Y. Chen and Stefano Lonardi, ed. (2009) Biological Data Mining. 656 pages. Published by Chapman & Hall/CRC, USA. ISBN: 978-1420086843. | Book | 2009 | |||
| 2 | Jake Y. Chen and Amandeep Sidhu, ed. (2007) Biological Database Modeling. 224 pages. Published by Artech House, Boston, MA, USA. ISBN: 978-1596932586. | Book | 2007 | |||
| 3 | Fan Zhang, Xiaogang Wu, and Jake Y. Chen* (2013) Computational Biomarker Discovery. Approaches in Integrative Bioinformatics – Towards Virtual Cell, pp. 355-386 | Refereed – Chapters | 2013 | |||
| 4 | Jake Y. Chen*, Heng Xu*, Pan Shi, Adam Culbertson, and Eric Meslin (2011) Ethics and Privacy Issues for Systems Biology Application in Predictive and Personalized Medicine. Handbook of Research on Computational and Systems Biology: Interdisciplinary Applications, pp. 1-27. | Refereed – Chapters | 2011 | |||
| 5 | Fan Zhang and Jake Y. Chen* (2011) Data Mining Methods in Omics-based Biomarker Discovery. Bioinformatics for Omics data: Methods and Protocols, pp. 511-526. | Refereed – Chapters | 2011 | |||
| 6 | Jake Y. Chen* and Tianxiao Huan (2010) ProteoLens: A Database-driven Visual Data Mining Tool for Network Biology. Systems Biology for Signaling Networks, pp. 857-876. | Refereed – Chapters | 2010 | |||
| 7 | Jieun Jeong and Jake Y. Chen* (2010) Techniques for Prioritization of Disease Genes. Computational Intelligence and Pattern Analysis in Biological Informatics, pp. 309-324. | Refereed – Chapters | 2010 | |||
| 8 | Jake Y. Chen*, Shailaja Taduri, and Frank Lloyd (2009) Design of an Online Physician-Mediated Personal Health Record System. Biomedical Data and Applications, Studies in Computational Intelligence, Vol. 224, pp. 265-279. | Refereed – Chapters | 2009 | |||
| 9 | Jake Y. Chen, Eunseog Youn, Sean D Mooney* (2009) Connecting Protein Interaction Data, Mutations and Disease using Bioinformatics. Methods in Molecular Biology: Computational Systems Biology, pp. 449-462. | Refereed – Chapters | 2009 | |||
| 10 | Xiaogang Wu and Jake Y. Chen* (2009) Molecular Interaction Networks: Topological and Functional Characterizations. Automation in Genomics and Proteomics: An Engineering Case-Based Approach, pp. 145-175. | Refereed – Chapters | 2009 | |||
| 11 | Amandeep Sidhu and Jake Y. Chen* (2007) Basic Concepts. Biological Database Modeling. Published by Artech House, pp. 1-8. | Refereed – Chapters | 2007 | |||
| 12 | Zhong Yan, Jake Y. Chen*, Josh Heyen, Lee W Ott, Cary Woods, Maureen A Harrington, and Mark G Goebl (2007) Data Management in Expression-based Proteomics. Biological Database Modeling. Published by Artech House, pp. 143-162. | Refereed – Chapters | 2007 | |||
| 13 | SudhaRani Mamidipalli and Jake Y. Chen* (2007) Protein-Protein Interactions: Concepts, Databases, Software Tools, and Biomedical Implications. Current Topics in Human Genetics: Studies of Complex Diseases. Published by World Scientific Publishing Co., pp. 539-562. | Refereed – Chapters | 2007 | |||
| 14 | Sangwoo Kim, Jake Y. Chen, Vincenzo Cutello, Doheon Lee (2016) DTMBIO 2016: The Tenth International Workshop on Data and Text Mining in Biomedical Informatics. Proceedings of ACM 2016 Conference on Information and Knowledge Management, pp. 2511-2512. | Editorial Articles in Books/Proceedings | 2016 | |||
| 15 | Mohammad Al Hasan, Luke Huan, Jake Y. Chen, and Mohammed Zaki (2011) BIOKDD’11: Workshop on Data Mining in Bioinformatics. Proceedings of the Tenth International Workshop on Data Mining in Bioinformatics, pp. 1-3. | Editorial Articles in Books/Proceedings | 2011 | |||
| 16 | Luke Huan, Jake Y. Chen, and Mohammed Zaki (2010) BIOKDD’10: Workshop on Data Mining in Bioinformatics. Proceedings of the Tenth International Workshop on Data Mining in Bioinformatics, pp. 1-3. | Editorial Articles in Books/Proceedings | 2010 | |||
| 17 | Vincent S. Tseng, Hui-Huang Hsu, and Jake Y. Chen (2009) Data Mining for Biomarker Discovery: The Time is Ripe. IEEE International Conference on Bioinformatics and Biomedicine Workshop 2009, pp. 195-196. | Editorial Articles in Books/Proceedings | 2009 | |||
| 18 | Jake Y. Chen and Stefano Lonardi (2009) Preface. Biological Data Mining, pp. ix-xii. | Editorial Articles in Books/Proceedings | 2009 | |||
| 19 | Stefano Lonardi, Jake Y. Chen, and Mohammed Zaki (2008) Editorial: 2008 International Workshop on Data Mining in Bioinformatics. Proceedings of the Eighth International Workshop on Data Mining in Bioinformatics, pp. 1-3. | Editorial Articles in Books/Proceedings | 2008 | |||
| 20 | Jake Y. Chen and Amandeep Sidhu (2007) Preface. Biological Database Modeling, pp. vii-x. | Editorial Articles in Books/Proceedings | 2007 | |||
| 21 | Jake Y. Chen, Stefano Lonardi, and Mohammed Zaki (2007) Editorial: BIOKDD ‘07: Workshop on Data Mining in Bioinformatics. Proceedings of the Seventh International Workshop on Data Mining in Bioinformatics, pp. 1-3. | Editorial Articles in Books/Proceedings | 2007 | |||
| 22 | Jake Y. Chen and Bradley S. Sherman (2005) Session Editorial: Computer Infrastructure for Systems Biology. Proceedings of the 18th International Conference on Systems Engineering. Published by IEEE Computer Society Press, pp. 283-285. | Editorial Articles in Books/Proceedings | 2005 | |||
| 23 | Warren T. Jones, Mathew J. Palakal, and Jake Y. Chen (2004) Editorial Message: Special Track on Bioinformatics. Proceedings of the 2004 ACM Symposium on Applied Computing, Nicosia, Cyprus, p. 101. | Editorial Articles in Books/Proceedings | 2004 | |||
| 24 | Jake Y. Chen and Thanh Nguyen (2021) Translational Bioinformatics and Artificial Intelligence. Intelligent Systems In Medicine and Health: The Role of AI (accepted) | Refereed – Chapters | 2021 | |||
| 25 | Zongliang Yue, Da Yan, Guimu Guo, Jake Y. Chen (2021) Network Mining. Modelling Transcriptional Regulation, Vol. 2328, p.139 | Refereed – Chapters | 2021 | |||
| 26 | Jun Deng, Thomas Hartung, Enrico Capobianco, Jake Y Chen and Frank Emmert-Streib (2022) Editorial: Artificial Intelligence for Precision Medicine. Frontiers in Artificial Intelligence (in press). | Editorial Articles in Books/Proceedings | 2022 | |||
| 27 | Da Yan, Hong Qin, Hsiang-Yun Wu, and Jake Y. Chen (2021) Editorial: AI-Enabled Data Science for COVID-19. Frontiers in Big Data, Vol. 4:802452. doi: 10.3389/fdata.2021.802452. | Editorial Articles in Books/Proceedings | 2021 | |||
| 28 | Da Yan, Zhaohui S. Qin, Debswapna Bhattacharya, and Jake Y. Chen (2022) Special Issue on BIOKDD 2021, IEEE/ACM Transactions on Computational Biology and Bioinformatics. Published by the IEEE Press. | Edited Conference Proceedings and Journal Special Issues | 2022 | |||
| 29 | Da Yan, Hong Qin, Hsiang-Yun Wu, and Jake Y. Chen (2021) AI-enabled Data Science for COVID-19, Frontiers in Artificial Intelligence. Published by the Frontiers Journals. | Edited Conference Proceedings and Journal Special Issues | 2021 | |||
| 30 | Jun Deng, Thomas Hartung, Enrico Capobianco, Jake Y. Chen, and Frank Emmert-Streib (2020) Artificial Intelligence in Precision Medicine, Frontiers in Artificial Intelligence. Published by the Frontiers Journals. | Edited Conference Proceedings and Journal Special Issues | 2020 | |||
| 31 | Da Yan, Hong Qin, Hsiang-Yun Wu, and Jake Y. Chen (2021) Special Issue on BIOKDD 2020, IEEE/ACM Transactions on Computational Biology and Bioinformatics. Published by the IEEE Press. | Edited Conference Proceedings and Journal Special Issues | 2021 | |||
| 32 | Da Yan, Xin Gao, Samah J. Fodeh, and Jake Y. Chen (2020) Special Issue on BIOKDD 2018 and DMBIH 2018, IEEE/ACM Transactions on Computational Biology and Bioinformatics. Published by the IEEE Press. | Edited Conference Proceedings and Journal Special Issues | 2020 | |||
| 33 | Xin Gao, Jake Y. Chen, and Mohammed Zaki, ed. (2018) Special Issue on BIOKDD Workshop 2016, IEEE/ACM Transactions on Computational Biology and Bioinformatics. Published by the IEEE Press. | Edited Conference Proceedings and Journal Special Issues | 2018 | |||
| 34 | Sarath Chandra Janga, Dongxiao Zhu, Jake Y. Chen, and Mohammed J. Zaki, ed. (2015) IEEE/ACM Transactions on Computational Biology and Bioinformatics. Published by the IEEE Press. | Edited Conference Proceedings and Journal Special Issues | 2015 | |||
| 35 | Jake Y. Chen and Vasant Honavar, ed. (2014) Proceedings of IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences. Published by the IEEE Press. | Edited Conference Proceedings and Journal Special Issues | 2014 | |||
| 36 | Sarath Janga, Dongxiao Zhu, Jake Y. Chen, and Mohammed Zaki, ed. (2014) Proceedings of the Thirteenth International Workshop on Data Mining in Bioinformatics. ACM 2014 | Edited Conference Proceedings and Journal Special Issues | 2014 | |||
| 37 | Gaurav Pandey, Huzefa Rangwala, George Karypis, Jake Y. Chen, and Mohammed Zaki, ed. (2013) Proceedings of the Twelfth International Workshop on Data Mining in Bioinformatics. ACM 2013, ISBN 978-1-4503-2327-7. | Edited Conference Proceedings and Journal Special Issues | 2013 | |||
| 38 | Vincent S. Tseng, Hui-Huang Hsu, and Jake Y. Chen, ed. (2012) Special Issue on Data Mining for Biomarker Discovery, International Journal of Data Mining in Bioinformatics. | Edited Conference Proceedings and Journal Special Issues | 2012 | |||
| 39 | Tamer Kahveci, Saeed Salem, Mehmet Koyuturk, Jake Y. Chen, and Mohammed Zaki, ed. (2012) Proceedings of the Eleventh International Workshop on Data Mining in Bioinformatics. ACM 2012, ISBN 978-1-4503-1552-4. | Edited Conference Proceedings and Journal Special Issues | 2012 | |||
| 40 | Jake Y. Chen, Mohammed Zaki, Mohammad Hasan, and Jun Huan, ed. (2011) Proceedings of the Tenth International Workshop on Data Mining in Bioinformatics. Published by ACM SIGKDD. | Edited Conference Proceedings and Journal Special Issues | 2011 | |||
| 41 | Vincent S. Tseng, Hui-Huang Hsu, and Jake Y. Chen, ed. (2010) Proceedings of the Second International Workshop on Data Mining in Bioinformatics. Published by IEEE press. | Edited Conference Proceedings and Journal Special Issues | 2010 | |||
| 42 | Luke Huan, Jake Y. Chen, and Mohammed Zaki, ed. (2010) Proceedings of the Ninth International Workshop on Data Mining in Bioinformatics. Published by ACM SIGKDD. | Edited Conference Proceedings and Journal Special Issues | 2010 | |||
| 43 | Vincent S. Tseng, Hui-Huang Hsu, and Jake Y. Chen, ed. (2009) Proceedings of the International Workshop on Data Mining in Bioinformatics. 34 pages. Published by IEEE press. | Edited Conference Proceedings and Journal Special Issues | 2009 | |||
| 44 | Stefano Lonardi and Jake Y. Chen, ed. (2008) Special Issue on Data Mining in Bioinformatics (BIOKDD 2007), Journal of Bioinformatics and Computational Biology, Vol. 6, No. 6. | Edited Conference Proceedings and Journal Special Issues | 2008 | |||
| 45 | Stefano Lonardi, Jake Y. Chen, and Mohammed Zaki, ed. (2008) Proceedings of the Eighth International Workshop on Data Mining in Bioinformatics. 70 pages. Published by ACM SIGKDD. | Edited Conference Proceedings and Journal Special Issues | 2008 | |||
| 46 | Amandeep S. Sidhu, Tharam S. Dillon, Elizabeth Chang, and Jake Y. Chen, ed. (2007) Special Issue on Ontologies for Bioinformatics, International Journal of Bioinformatics Research and Applications, Vol. 3, No. 3. | Edited Conference Proceedings and Journal Special Issues | 2007 | |||
| 47 | Jake Y. Chen, Stefano Lonardi, and Mohammed Zaki, ed. (2007) Proceedings of the Seventh International Workshop on Data Mining in Bioinformatics. 87 pages. Published by ACM SIGKDD. | Edited Conference Proceedings and Journal Special Issues | 2007 | |||
| 48 | Katsuhisa Horimoto, Jake Chen, and Amy Chan, ed. (2004) Applications of Informatics and Cybernetics in Science and Engineering, Proceedings of the 8th World Multi-Conference on Systemics, Cybernetics and Informatics (Vol. VII). ISBN: 980-6560-13-2. | Edited Conference Proceedings and Journal Special Issues | 2004 |