[1] Jake Y. Chen and Stefano Lonardi, ed. (2009) Biological Data Mining. 656 pages. To be published by Chapman & Hall/CRC, USA. ISBN: 978-1420086843.
[2] Jake Y. Chen and Amandeep Sidhu, ed. (2007) Biological Database Modeling. 224 pages. Published by Artech House, Boston, MA, USA. ISBN: 978-1596932586.
Edited Proceedings (3)
[3] 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.
[4] 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.
[5] 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 Journal Special Issues (3)
[6] Stefano Lonardi and Jake Y. Chen, ed. (2009) Special Issue on Data Mining in Bioinformatics (BIOKDD 2008), IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 6, No. 4.
[7] 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.
[8] 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.
Refereed –Journal Articles (25)
[9] Jiao Li, Xiaoyan Zhu, and Jake Y. Chen (2009) Building Disease-specific Drug-Protein Connectivity Maps from Molecular Interaction Networks and PubMed Abstracts, PLoS Computational Biology. (Accepted) (ISI journal impact factor = 7.7)
[10] Sudhir R. Chowbina, Xiaogang Wu, Fan Zhang, Peter M. Li, Ragini Pandey, Harini N. Kasamsetty, and Jake Y. Chen (2009) HPD: An Online Integrated Human Pathway Database Enabling Systems Biology Studies. BMC Bioinformatics. (Accepted) (ISI journal impact factor = 4.39)
[11] Jake Y. Chen, SudhaRani Mamidipalli, and Tianxiao Huan (2009) HAPPI: an Online Database of Comprehensive Human Annotated and Predicted Protein Interactions. BMC Genomics, Vol. 10, Supplement 1, S16 (ISI journal impact factor = 4.18)
[12] Jiao Li, Xiaoyan Zhu, and Jake Y. Chen (2009) Discovering Novel Breast Cancer Drug Candidates from Biomedical Literature. International Journal of Data Mining and Bioinformatics. (In press)
[13] Mingyi Wang and Jake Y. Chen (2009) A GMM-IG Framework for Selecting Genes as Expression Panel Biomarkers. Artificial Intelligence in Medicine. (In press) (ISI journal impact factor = 1.83)
[14] Huajun Chen, Li Ding, Zhaohui Wu, Tong Yu, Lavanya Dhanapalan, and Jake Y. Chen (2009) Semantic Graph Mining for Biomedical Network Analysis: an Overview. Briefings in Bioinformatics, Vol. 10, No. 2, pp. 177-192. (ISI journal impact factor = 4.42)
[15] Huian Li and Jake Y. Chen (2009) Improved Biomedical Document Retrieval System with PubMed Term Statistics and Expansions. International Journal of Computational Intelligence in Bioinformatics and Systems Biology, Vol. 1, No. 1, pp. 74-89.
[16] Sudipto Saha, Scott H. Harrison, and Jake Y. Chen (2009) Dissecting the Human Plasma Proteome and Inflammatory Response Biomarkers. Proteomics, Vol. 9, No. 2, pp. 470-484. (ISI journal impact factor = 5.48)
[17] Jake Y. Chen, Mohammed Zaki, and Stefano Lonardi (2008) BIOKDD 2008: A Workshop Report on Data Mining in Bioinformatics. SIGKDD Explorations, Vol. 10, No. 2, pp. 51-53.
[18] Tianxiao Huan, Andrey Sivachenko, Scott H. Harrison, and Jake Y. Chen (2008) ProteoLens: a Visual Analytic Tool for Multi-scale Database-driven Biological Network Data Mining. BMC Bioinformatics, Vol. 9, S5, pp. 1-13. (ISI journal impact factor = 4.39)
[19] Sudipto Saha, Scott H. Harrison, Changyu Shen, Haixu Tang, Predrag Radivojac, Randy J. Arnold, Xiang Zhang, and Jake Y. Chen (2008) HIP2: An Online Database of Human Plasma Proteins from Healthy Individuals. BMC Medical Genomics, 2008, Vol. 1, 12.
[20] Qian You, Shiaofen Fang, and Jake Y. Chen (2008) GeneTerrain: Visual Exploration of Differential Gene Expression Profiles Organized in Native Biomolecular Interaction Networks. Information Visualization, doi: 10.1057 (advanced online publication 6 March 2008).
[21] Stefano Lonardi and Jake Y. Chen (2008) International Workshop on Data Mining in Bioinformatics (BIOKDD) 2007: Introduction. Journal of Bioinformatics and Computational Biology, Vol. 6, No. 6, pp. v-vi.
[22] Lee W. Ott, Katheryn A. Resing, Alecia W. Sizemore, Joshua W. Heyen, Ross R. Cocklin, Nathan M. Pedrick, H. Cary Woods, Jake Y. Chen, Mark G. Goebl, Frank A. Witzmann, and Maureen A. Harrington (2007) Tumor Necrosis Factor-alpha and Interleukin-1 Induced Cellular Responses: Coupling Proteomic and Genomic Information. Journal of Proteome Research, Vol. 6, Issue 6, pp. 2176-2185. (ISI journal impact factor = 5.68)
[23] Lavanya Dhanapalan and Jake Y. Chen (2007) A Case Study of Integrating Protein Interaction Data using Semantic Web Technology. International Journal of Bioinformatics Research and Applications, Vol. 3, No. 3, pp. 286-302.
[24] Jake Y. Chen, Zhong Yan, Changyu Shen, Dawn P. G. Brown, and Mu Wang (2007) A Systems Biology Approach to The Study Of Cisplatin Drug Resistance In Ovarian Cancers. Journal of Bioinformatics and Computational Biology, Vol. 5, Issue 02A, pp. 383-405.
[25] Megan Sickmeier, Justin Hamilton, Tanguy LeGall, Vladimir Vacic, Marc Cortese, Agnes Tantos, Beata Szabo, Peter Tompa, Jake Chen, Vladimir Uversky, Zoran Obradovic, A Keith Dunker (2007) DisProt: The Database of Disordered Proteins. Nucleic Acids Research, Vol. 35 (Database issue): pp. 786-93. (ISI journal impact factor = 6.95)
[26] Tharam S. Dillon, Elizabeth Chang, Amandeep S. Sidhu, and Jake Y. Chen (2007) Ontologies for Bioinformatics I. International Journal of Bioinformatics Research and Applications, Vol. 3, No. 3, pp. 261-267.
[27] Zsuzsanna Dosztányi, Jake Y. Chen, A. Keith Dunker, István Simon, and Peter Tompa (2006) Disorder and Sequence Repeats in Hub Proteins and Their Implications for Network Evolution, Journal of Proteome Research, Vol. 5, Issue 11, pp. 2985-2995. (ISI journal impact factor = 5.68)
[28] Changyu Shen, Lang Li, Jake Y. Chen (2006) A Statistical Framework to Discover True Associations from Multi-protein Complex Pull-down Proteomics Data Sets. Proteins: Structure, Function, and Bioinformatics, Vol. 64, Issue 2, pp. 436-43. (ISI journal impact factor = 3.73)
[29] Jake Y. Chen and Andrey Y. Sivachenko (2005) Data Mining in Protein Interactomics. IEEE Magazine in Biology and Medicine, Vol. 24, No. 3, pp. 95-102. (ISI journal impact factor = 1.23)
[30] Susie Stephens, Jake Y. Chen, Marcel Davidson, Shiby Thomas, and Barry M. Trute (2005) Oracle Database 10g: A Platform for BLAST Search and Regular Expression Pattern Matching in Life Sciences, Nucleic Acids Research, Vol. 33, Database Issue, pp. 675-679. (ISI journal impact factor = 7.55)
[31] Susie Stephens, Jake Y. Chen, and Shiby Thomas (2004) ODM BLAST: Sequence Homology Search in the RDBMS. IEEE Data Engineering Bulletin, Vol. 27, Issue 3, pp. 20-23.
[32] Jake Y. Chen (2004) Book Review: Digital Code of Life—How Bioinformatics is Revolutionizing Science, Medicine, and Business. Briefings in Bioinformatics, Vol. 5, Issue 3, pp. 305-307. (ISI journal impact factor = 4.42)
[33] Jake Y. Chen and John Carlis (2003) Genomic Data Modeling. Information Systems, Vol. 28, Issue 4: (Special Issue on Data Management in Bioinformatics), pp. 287-310. (ISI journal impact factor = 1.68)
Refereed – Proceedings Articles (22)
[34] Fan Zhang and Jake Y. Chen (2009) A Neural Network Approach to Developing Multi-Marker Panels for Breast Cancer Based on LC/MS/MS Proteomics Profiles, Proceedings of the 22nd IEEE Symposium on Computer-Based Medical Systems. (Accepted)
[35] Amandeep Sidhu, Fan Zhang, Scott Harrison, Peter Hussey, and Jake Y. Chen (2009) Towards an Ontology for Mass-spectrometry based Clinical Proteomics, Proceedings of the 22nd IEEE Symposium on Computer-Based Medical Systems. (Accepted)
[36] 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. (Accepted)
[37] 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. (Accepted)
[38] Qian You, Shiaofen Fang, Snehasis Mukhopadhyay, Harsha Vaka, and Jake Y. Chen (2009) Visualizing a Correlative Multi-level Graph of Biology Entity Interactions, Proceedings of Workshop on Intelligent Biomedical Information Systems at the 12th International Conference on Network-Based Information Systems. (In press)
[39] John Springer and Jake Y. Chen (2009) Toward Ontology-Driven Omics Data Integration in Current Database Management Systems, Proceedings of Workshop on Intelligent Biomedical Information Systems at the 12th International Conference on Network-Based Information Systems. (In press)
[40] 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%)
[41] 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)
[42] 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)
[43] 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)
[44] 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)
[45] 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%)
[46] 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%)
[47] 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)
[48] 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%)
[49] Jake Y. Chen, Andrey Y. Sivachenko, and Lang Li (2004) High-throughput Protein Interactome Data: Minable or Not? Proceedings of the 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%, out of 26 submissions)
[50] 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. (Acceptance rate: 50%)
[51] 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%)
[52] 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%)
[53] 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.
[54] 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.
[55] 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.
Refereed – Book Chapters (6)
[56] Jake Y. Chen, Shailaja Taduri, and Frank Lloyd (2009) Design of an Online Physician-Mediated Personal Health Record System. Biomedical Data and Applications. (In press)
[57] 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.
[58] 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.
[59] Amandeep Sidhu and Jake Y. Chen (2007) Basic Concepts. Biological Database Modeling. Published by Artech House, pp. 1-8.
[60] 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.
[61] 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.
Editorial Articles in Books/Proceedings (6)
[62] Jake Y. Chen and Stefano Lonardi (2009) Preface. Biological Data Mining. (To appear)
[63] 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.
[64] Jake Y. Chen and Amandeep Sidhu (2007) Preface. Biological Database Modeling, pp. vii-x.
[65] 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.
[66] 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.
[67] 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.
Dissertation (1)
[68] Jake Y. Chen (2001) PhD Dissertation: A Bioinformatics Discovery-oriented Computing Framework. 172 pages. UMI Microfilm 3020585.