[1] Saha, Sudipto, 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, (accepted)
[2] Wang, Mingyi 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, Sanya, Hainan, China. (accepted. Acceptance rate: ~15%, out of >500 submissions)
[3] Kasamsetty, Harini, 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, (accepted. Acceptance rate: 24%, 9 out of 38 submissions)
[4] Li, Jiao, 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, (accepted. Acceptance rate: 24%, 9 out of 38 submissions)
[5] Huian Li and Jake Y. Chen (2008) Improved Biomedical Document Retrieval System with PubMed Term Statistics an Expansions, International Journal of Computational Intelligence in Bioinformatics and Systems Biology, (Accepted)
[6] You, Qian, Shiaofen Fang, and Jake Y. Chen (2008) GeneTerrain: Visual Exploration of Differential Gene Expression Profiles Organized in Native Biomolecular Interaction Networks. Information Visualization, (In press)
[7] Ott, Lee W, 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, p2176-2185.
[8] 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, p286-302.
[9] Chen, Jake Yue, 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, p383-405.
[10] Sickmeier, Megan, 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): D786-93.
[11] Dosztányi, Zsuzsanna, 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, p2985-2995.
[12] Chen, Jake Yue, 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, p389-398. (Acceptance rate: 19%, out of 154 submissions)
[13] Shen, Changyu, 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, p436-43.
[14] Chen, Jake Yue, 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, p173-179. (Acceptance rate: 32%)
[15] Chen, Jake Yue, Changyu Shen, and Andrey Sivachenko (2006) Mining Alzheimer Disease Relevant Proteins from Integrated Protein Interactome Data. Pacific Symposium on Biocomputing, Vol. 11, p367-378 (Acceptance rate: 20%)
[16] Shen, Changyu, 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: p167-174. (Acceptance rate: 12%, out of 246 submissions)
[17] Chen, Jake Yue and Andrey Y. Sivachenko (2005) Data Mining in Protein Interactomics, IEEE Magazine in Biology and Medicine, Vol. 24, No.3: p95-102.
[18] Chen, Jake Yue, 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, p110-114. (Acceptance rate: 35%)
[19] Stephens, Susie, 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: p675-679.
[20] Stephens, Susie, Jake Y. Chen, and Shiby Thomas (2004) ODM BLAST: Sequence Homology Search in the RDBMS, IEEE Data Engineering Bulletin, Vol. 27, issue 3: p20-23.
[21] Chen, Jake Yue, Andrey Y. Sivachenko, and Lang Li (2004) High-throughput Protein Interactome Data: Minable or Not?, Proceedings of the 4th ACM SIGKDD Workshop on Data Mining in Bioinformatics (BioKDD 2004) at the International Conference on Knowledge Discovery and Data Mining, Seattle, WA, p18-23. (Acceptance rate: 38%, out of 26 submissions)
[22] Chen, Jake Yue (2004) Experience with Processing and Exploration of High-throughput Protein Interaction Data, Session on Systems Biology and Bioinformatics, Proceedings of the 8th World Multi-Conference on Systemics, Cybernetics and Informatics, Orlando, FL, Vol. VII, p41-45.
[23] Chen, Jake Yue, 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, p229-234. (Acceptance rate: 18%)
[24] Chen, Jake Yue and John Carlis (2003) Similar_Join: Extending DBMS with a Bio-specific Operator. Proceedings of the 18th ACM Symposium on Applied Computing, Melbourne, Florida, p109-114. (Acceptance rate: 33%)
[25] Chen, Jake Yue and John Carlis (2003) Genomic Data Modeling. Information Systems, Vol. 28, Issue 4: (Special Issue on Data Management in Bioinformatics), p287-310.
[26] Chen, Jake Yue and John Carlis (2002) Managing Bioinformatics Challenges in Expression Microarray Sequence Selection Projects. Proceedings of the 2nd Chinese Conference on Bioinformatics, Beijing, China.
[27] Chen, Jake Yue 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.
[28] Chen, Jake Yue (2001) PhD Thesis: A Bioinformatics Discovery-oriented Computing Framework.
[29] Chen, Yue, Libby Shoop, John Carlis, and John Riedl (2001) A High-throughput System to Resolve Inconsistent Reading Frame Predictions for Expressed Sequence Tags. Workshop on Inconsistency in Data and Knowledge at the International Joint Conference on Artificial Intelligence (IJCAI), Seattle, WA.
[30] Wu, Xiaogang and Jake Y. Chen (2008) Molecular Interaction Networks: Topological and Functional Characterizations, in Automation in Genomics and Proteomics: An Engineering Case-Based Approach. To appear.
[31] Jake Y. Chen, Eunseog Youn, Sean D Mooney (2008) Connecting Protein Interaction Data, Mutations and Disease using Bioinformatics, in Methods in Molecular Biology: Computational Systems Biology. To appear.
[32] Jake Y. Chen and Shailaja Taduri (2008) Design of an Online Physician-Mediated Personal Health Record System, in Biomedical Data and Applications—Studies in Computational Intelligence Book Series. To appear.
[33] Sidhu, Amandeep, Jake Y. Chen (2007) Basic Concepts, in Biological Database Modeling. Published by Artech House.
[34] Yan, Zhong, Jake Y. Chen, Josh Heyen, Lee W Ott, Cary Woods, Maureen A Harrington, and Mark G Goebl (2007) Data Management in Expression-based Proteomics, in Biological Database Modeling. Published by Artech House.
[35] Mamidipalli, SudhaRani and Jake Y. Chen (2007) Protein-Protein Interactions: Concepts, Databases, Software Tools, and Biomedical Implications, in Current Topics in Human Genetics: Studies of Complex Diseases. Published by World Scientific Publishing Co.
[36] Jake Y. Chen and Amandeep Sidhu (2007) Preface, Biological Database Modeling. p. vii-x.
[37] Jake Y. Chen, Stefano Lonardi, and Mohammed Zaki (2007) Editorial: BIOKDD ‘07: Workshop on Data Mining in Bioinformatics. Proceedings of the 7th International Workshop on Data Mining in Bioinformatics, p1-3.
[38] Dillon, Tharam S., Elizabeth Chang, Amandeep S. Sidhu, and Jake Y. Chen (2007) Editorial: Ontologies for Bioinformatics I. International Journal of Bioinformatics Research and Applications, Vol. 3, No. 3. P261-267.
[39] Jake Y. Chen and Bradley S. Sherman (2005) Session Editorial: Computer Infrastructure for Systems Biology. In Proceedings of the 18th International Conference on Systems Engineering. Published by IEEE Computer Society Press, p283-285.
[40] Jake Y. Chen (2004) Book Review: Digital Code of Life—How Bioinformatics is Revolutionizing Science, Medicine, and Business, by Glyn Moody (John Wiley & Sons, Inc, New Jersey 2004). In Briefings in Bioinformatics, Vol 5, Issue 3, p305-307.
[41] Warren T. Jones, Mathew J. Palakal, and Jake Y. Chen (2004) Editorial Message: Special Track on Bioinformatics. In Proceedings of the 2004 ACM Symposium on Applied Computing, Nicosia, Cyprus: p101.
[1] Jake Y. Chen and Stefano Lonardi, ed. (2008) Biological Data Mining. Approximately 400 pages. To be published by Prentice Hall/Chapman, USA.
[2] Jake Y. Chen and Amandeep Sidhu, ed. (2007) Biological Database Modeling. 224 pages. Published by Artech House, Boston, MA, USA. ISBN: 978-1596932586
[3] Nagib Callos, Katsuhisa Horimoto, Jake Chen, and Amy Kit Sze 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). Published by the International Institute of Informatics and Systemics, Orlando, FL, USA. ISBN: 980-6560-13-2.
[1] Jake Y. Chen, Yaoqi Zhou, Sunil Badve, and Mu Wang (2008) Indiana Center for Systems Biology and Personalized Medicine. 2008 IUPUI Solutions Conference, March 18, 2008.
[2] Andrey Sivachenko, Tianxiao Huan, Scott Harrison, and Jake Y. Chen (2008) ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining. The Fifth Annual Conference of the MidSouth Computational Biology and Bioinformatics Society, February 23, 2008.
[3] Scott Harrison, Peter Hussey, Sudipto Saha, and Jake Y. Chen (2007) A Data Model for Managing Experimental Metadata for Mass Spectrometry-Based Clinical Proteomics, Clinical Proteomic Technologies for Cancer Annual Meeting, Rockville, MA, Oct 24-5, 2007.
[4] Scott Harrison, Sudipto Saha, Xiang Zhang, and Jake Y. Chen (2007) Proteomics Pipeline Infrastructure at IUPUI for the CPTAC Purdue University Research Team, Clinical Proteomic Technologies for Cancer Annual Meeting, Rockville, MA, Oct 24-5, 2007.
[5] Jiliang Li and Jake Y. Chen (2008) A Systems Biology Informatics Approach to Compare Proteomics Profiles in Bone Induced by Loading and Fatigue Loading, 54th Annual Meeting of the Orthopedic Research Society, San Francisco, CA, March 2-5, 2008.
[6] Mingyi Wang, Steve Valentine, Samiran Ghosh, Nasser Hanna, Zane T. Hammoud, and Jake Y. Chen (2007) An Integrated Method to Identify Gene Signatures for Lung Cancer Tissue Classifications, Indy Midwest Regional Bioinformatics Conference, Indianapolis, IN, May 31-June 2, 2007.
[7] Sudipto Saha and Jake Y. Chen (2007) A Catalogue of Human Plasma Proteins for Clinical Proteomics Applications, Indy Midwest Regional Bioinformatics Conference, Indianapolis, IN, May 31-June 2, 2007.
[8] Harini Kasamsetty and Jake Y. Chen (2007) Towards an Integrated Comprehensive Human Pathway Database Resource, Indy Midwest Regional Bioinformatics Conference, Indianapolis, IN, May 31-June 2, 2007.
[9] Jiliang Li and Jake Y. Chen (2007) Proteomics Changes Induced by Mechanical Loading in Bone, Abstract, 37th International Sun Valley Workshop On Skeletal Tissue Biology, Sun Valley, ID, Aug 5-8, 2007.
[10] Jake Y. Chen (2006) Use of High-Performance Computers to Develop Biological Network Data Management and Visualization Software, Poster Session, Supercomputing Conference (SC 06), Tampa, FL, Nov 13-16, 2006.
[11] Jake Y. Chen (2006) Human Disease Targetome: a New Approach to High-throughput Drug Target Discovery, Poster Session, Innovention 06, Indianapolis, IN, June 12-13, 2006.
[12] Jake Y. Chen (2006) Enabling "Fat Queries" on a TeraGrid-powered Systems Biology Data Warehouse, TeraGrid ‘06, Indianapolis, IN, June 12-15, 2006.
[13] Arti Singh and Jake Y. Chen (2006) Integrated Analysis of Essential Genes and Network Hubs as Potential Druggable Targets, Poster Session, 3rd Indiana Bioinformatics Conference, Indianapolis, IN, May 20-21, 2006.
[14] Jake Y. Chen (2005) Novel Computational Drug Target Discovery using Discovery Bioinformatics Platforms, Indiana University Statewide IT Conference, Indianapolis, September 28-29, 2005.
[15] Jake Y. Chen (2005) Mining Protein Interactomes: A Case Study of Bio-discovery Informatics, Changchun International Bioinformatics Workshop, Changchun, Jilin, China, July 5-7, 2005.
[16] Muralidharan Kannan, Mathew Palakal, Sudhanshu Patwardhan, Santosh K. Mlshra, Subhra K. Biswas, Jake Y. Chen (2005) Inflammation BioKW: A Case Study in Knowledge Discovery from Heterogeneous Biological Databases through Warehousing. Poster Session, 13th International Conference on Intelligent Systems in Molecular Biology, Detroit, Michigan, USA, June 25-29, 2005.
[17] Vladimir Vacic, Shelley Riggen, Amy Lewis, Elizabeth Patterson, Megan Sickmeier, Jason Baird, Justin Hamilton, Denise Kim, Marc Cortese, Jake Y, Chen, Predrag Radivojac, Vladimir Uversky, Slobodan Vucetic, Zoran Obradovic, and Keith Dunker (2004) DisProt: A Database of Protein Disorder. Poster Session, Indiana Proteomics Symposium, Bloomington, IN, USA, October 15, 2004.
[18] Jake Y. Chen (2004) Protein Interactomics. Poster Session, Indiana Technology Summit VII, Indianapolis, IN, USA, September 29, 2004.
[19] Jake Y. Chen (2004) Mining Protein Protein Interactions. Exhibition representing Indiana University School of Informatics. Indiana State Fair ‘04, Indianapolis, IN, USA, August 11-22, 2004.
[20] Jake Y. Chen (2004) Protein Interactomics—Mining Functional Links between Proteins. Poster Session, Indiana Health Innovention ‘04, Indianapolis, IN, USA, June 16-17, 2004.
[21] Jake Y. Chen (2004) Biological Data Warehouses—a Platform for Integrative Systems Biology. Poster Session, 1st Indiana Bioinformatics Conference, Indianapolis, IN, USA, May 27, 2004.
[22] Susie Stephens, Marcel Davidson, and Jake Y. Chen (2003) Sequence Search Capabilities in the Database. Conference presentation, Oracle Life Sciences User Group Meeting at OracleWorld Conference 2003, San Francisco, CA, USA, September 10, 2003.
[23] Sudhir Sahasrabudhe and Jake Y. Chen (2003) Extracting Biological Information from System-scale Protein Interactome Data. Tutorial Session, 11th International Conference on Intelligent Systems in Molecular Biology, Brisbane, Australia, USA, June 29-July 3, 2003.
[24] Jake Y. Chen (2002) Managing High-throughput Human Proteomics Data. Conference presentation, Cambridge Healthtech Institute's Beyond Genome: 11th Annual Bioinformatics and Genome Research Conference, San Diego, CA, USA, June 9-12, 2002.
[25] Yue Chen, Elizabeth Shoop, Ed H Chi, Sheila St. Cyr, Sopheak Sim, Juan Munoz, John Riedl, Ernest Retzel, and John Carlis (1998) Developing an Automated System for High Throughput Reading Frame Assignment on Expressed Sequence Tags. Poster Session, 6th International Conference on Intelligent Systems for Molecular Biology, Montreal, Quebec, Canada, June 28-July 1, 1998.
[26] Yue Chen (1996) Identifying a Zinc Finger Motif from a Human EST Sequence with an Unusually High Content of Ambiguous Nucleotides. Poster Session, 4th International Conference on Intelligent Systems for Molecular Biology, St. Louis, MO, USA, June 12-15, 1996.
[1] C-Map: Connectivity Map Web Server. (2008) Developed at Indiana University. http://bio.informatics.iupui.edu/cmaps/
[2] HIP2: A Database for Health Human Individual’s Integrated Plasma Proteome. (2007) Developed at Indiana University. http://bio.informatics.iupui.edu/HIP2/
[3] HAPPI Database: Human Annotated and Predicted Protein Interactions. (2006) Developed at Indiana University. http://bio.informatics.iupui.edu/HAPPI/
[4] ProteoLens: a Visual Data Mining and Querying Tool. (2006) Developed at Indiana University and Salt Lake City. http://bio.informatics.iupui.edu/proteolens/
[5] Mining Protein Interaction Networks. Sole inventor. US patent application #20070072226 (status pending).
[6] Sequence Selection Methods for High-density Expression Microarrays. US patent application filed in Jan 2001 with Michael Mittmann and Hui Wang at Affymetrix, Inc., Santa Clara, CA.
[7] A Relational Database Operator to perform Biological Sequence Similarity Search. Sole inventor. US patent Filed in Jan 2001.