Keynote/Plenary Speech (2)

[1]      Plenary Speech, “ProteoLens: a Visual Analytic Tool for Multi-scale Database-driven Biological Network Data Mining” (February 2008) Fifth Annual Conference of the MidSouth Computational Biology and Bioinformatics Society, Oklahoma, OK.

[2]      Keynote Speech, “Translational Systems Biology: A Prelude” (November 2007) 2nd IEEE International Workshop on Data Mining in Bioinformatics, at the IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Fremont, CA.

Invited Conference Panel Presentations (7)

[3]      “Can We Overcome the Challenges in Cancer Biomarker Development through CTSA at Indiana?” (February 2009) Panel: Biomedical Informatics Research and Education, at Fourth Annual iConference 2009, University of North Carolina at Chapel Hill, NC.

[4]      “Translational Bioinformatics: Challenges for New Computational Tools” (October 2008) Panel: Computational Biology, at Innovation in Life Science & Healthcare Research & Product Development Meeting, Philadelphia, PA.

[5]      “Indiana Systems Biology Research Supporting Personalized Medicine” (September 2008) Panel: Personalized Health Care at State of Our Health—an Indiana Leadership Forum on Health Care Quality Measurement and Improvement, Indianapolis, IN.

[6]      “Graduate Bioinformatics Curricular Development at Indiana University” (June 2008) Panel: Developing Adequate Curricula for Training the Next Generation of Computational and Systems Biologist. International Bioinformatics Workshop ’08, Kunming, Yunnan, China.

[7]      “High-performance Database Computing in Biomedical Informatics” (December 2007) Panel: Research Database Computing, NSF Workshop on Biomedical Informatics, Portland, OR.

[8]      “Collaborative Research: What we learned from the Purdue-IU Clinical Proteomics Grant Application and where the Informatics Opportunities are” (October 2006) Panel: Brilliant Minds, Powerful Technology & Life Sciences: Pushing the Frontiers of Knowledge for Indiana, at Indiana Technology TechPoint Summit 9 Conference, Indianapolis, IN.

[9]      “Protein Informatics: Turning Data into Knowledge” with Emanuel Petricoin, Eric Neumann, Sudhir Sahasrabudhe, and Jacquelyn Fetrow. (September 2002) Webcast, Bio.com Monthly InFocus Panel, various locations on the World Wide Web.

Invited Conference/Workshop/Symposium Presentations (18)

[10]  “Network Multi-marker Panels towards Next-generation Robust and Interpretable Biomarkers” (September 2009) CHI Accelerating Discovery and Advancing Personalized Therapy Conference, Washington, DC. (Accepted)

[11]  “Cancer Clinical Proteomics” (May 2009) Informatics, Biomedical Informatics, and Translational Research Mini-Conference, Windber Research Institute, Windber, PA.

[12]  “Translational Systems Biology” (April 2009) Mini-symposium of DARPA Delegates and IUPUI Signature Center Directors, Indiana University – Purdue University, Indianapolis, IN.

[13]  “Web 2.0 Tools and its Impact on the Quality of Teaching and Learning” (April 2009) Annual Edward C. Moore Symposium, Indiana University – Purdue University, Indianapolis, IN.

[14]  “Translational Systems Biology: Bridging Gaps for Genome Medicine” (February 2009) 16th CHI International Molecular Medicine Tri-Conference, San Francisco, CA.

[15]  “Bio-computing and Knowledge Discovery of Molecular Networks” (December 2008) e-Bioinformatics Workshop at the 4th IEEE International Conference on E-Science, Indianapolis, IN.

[16]  “Characterizing the Human Plasma Proteome” (October 2008) Midwest Computational Biology and Bioinformatics Symposium, University of Illinois, Urbana-Champion, IL.

[17]   “A Translational Systems Biology Approach to Panel Biomarker Discoveries” (October 2008) Biomarker Discovery Summit 2008, Philadelphia, PA.

[18]  “Translational Bioinformatics: Tools Bridging Genomics Discovery and Biomedical Applications” (June 2008) International Bioinformatics Workshop 2008 (IBW ’08), Yunnan University, Kunming, Yunnan, China.

[19]   “Molecular Connectivity and Network Biology Tools for Complex Disease Studies” (April 2008) Indiana University – University of Notre Dame Biomedical Research Collaboration Mini-Symposium, Biocomplexity Institute, University of Notre Dame, South Bend, IN.

[20]  “Translational Bioinformatics” (September 2007) Purdue – Intel Bioscience Technology Summit, Bindley Bioscience Center, Purdue University Discovery Park, West Lafayette, IN.

[21]  “Introduction to BIOKDD ’07” (August 2007) 7th International Workshop on Data Mining in Bioinformatics, ACM SIGKDD Conference, San Jose, CA.

[22]  “Computational Systems Biology: New Research Opportunities & Applications” (June 2007) Changchun International Workshop on Systems Biology, Jilin University, Changchun, China.

[23]  “Network Biology Research: Connecting the Dots in Biology” (February 2007) Indiana University School of Informatics Bioinformatics Faculty Retreat, Bradford Woods, IN.

[24]  “Informatics-driven Systems Biology Research Supporting Translational Biomedical Discoveries” (November 2006) Indiana State Legislature Tech Conference, Indianapolis, IN.

[25]  “Enabling ‘Fat Queries’ on a TeraGrid-powered Systems Biology Data Warehouse” (June 2006) TeraGrid Conference ‘06, Indianapolis, IN.

[26]  “Mining Protein Interactomes: A Case Study of Bio-discovery Informatics” (July 2005) Changchun International Bioinformatics Workshop, Jilin University, Changchun, Jilin, China.

[27]  “Sequence Search Capabilities in the Database” (September 2003) Invited Presentation, Oracle Life Sciences User Group Meeting, OracleWorld Conference 2003, San Francisco, CA.

Invited Seminars – International (17)

[28]  “Systems Biology Approaches to Biomarker Discovery” (July 2009) Mathematics Department, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China. (Accepted)

[29]  “Bioinformatics for Biomarker Discoveries and Personalized Medicine” (June 2009) College of Life Sciences, Capital Normal University, Beijing, China. (Accepted)

[30]  “Computational Opportunities in Clinical Proteomics and Biomarker Discoveries” (June 2008) Institute of Computer Science & Technology, Chinese Academy of Sciences, Beijing, China.

[31]  “Bioinformatics towards Human Disease-related Studies: Trends and Opportunities” (June 2008) Capital Normal University, Beijing, China.

[32]  “Developing Translational Bioinformatics Tools for Biomedical Applications” (June 2008) College of Life Sciences, Shandong University of Technology, Shandong, China.

[33]   “Development of Systems Biology Resources and Applications at IUPUI” (July 2007) Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.

[34]  “Computational Systems Biology: Research Opportunities & Applications for Post-genome Bioinformatics” (July 2007) School of Medicine, Sun Yat-Sen University, Guangzhou, China.

[35]  “Post-genome Bioinformatics Applications in Cancer Research” (June 2007) Invited Seminar, School of Basic Medical Sciences, Dalian Medical University, Dalian, Liaoning Province, China.

[36]  “Network Biology and Informatics” (June 2007) College of Life Sciences, Shandong University, Jinan, Shandong Province, China.

[37]  “Systems Biology Informatics Supporting Translational Disease-specific Studies” (August 2006) Center for Bioinformatics, College of Life Sciences, Peking University, Beijing, China.

[38]  “Systems Biology Informatics: Translational Bio-computing for Disease-specific Studies” (July 2006) Department of Computer Science & Technology, Tsinghua University, Beijing, China.

[39]  “Bio-discovery Informatics” (July 2005) Invited Seminar, Center for Bioinformatics, College of Life Sciences, Peking University, Beijing, China.

[40]  “Systems Biology Informatics: Shaping the Future Landscape of Biology using Computers” (July 2005) School of Information Sciences, Northeastern University, Shenyang, China.

[41]  “Bio-discovery Informatics: A Case Study in Integrative Network Biology” (April 2005) Center for Information Biology and the DNA Data Bank of Japan (DDBJ), National Institute of Genetics of Japan, Mishima, Japan.

[42]  “Protein Interactomics: An Emerging Frontier in Bioinformatics” (August 2004) College of Life Sciences, Peking University Beijing, China.

[43]   “Establishing Bioinformatics Infrastructure in Support of Biological Knowledge Discoveries” (March 2002) Bioinformatics Center, Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai, China.

[44]  “Managing Genomic Data” (May 2000) Center for Bioinformatics, Peking University, Beijing, China.

Invited Seminars – US National (23)

[45]  “Network and Systems Biology: Power Tools for Post-genome Biomarker Discovery” (May 2009) Windber Research Institute, Windber, PA.

[46]  “Bioinformatics and Genome Medicine” (May 2009) College of Information Sciences and Technology, Penn State University, College Station, PA.

[47]  “Molecular Network Pharmacology: Enabling Future Drug Discovery through Translational Systems Biology” (April 2009) College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR.

[48]  “Translational Bioinformatics: Computational Tools Enabling Genome Medicine” (July 2008) School of Medicine, University of California, San Diego, CA.

[49]  “Translational Systems Biology: Connectivity, Network Models, & Panel Biomarker Discoveries” (April 2008) Computational Biology and Bioinformatics Graduate Program Colloquium, Northwestern University, Evanston, IL.

[50]  “Translational Bioinformatics and Systems Biology” (October 2007) Department of Computer Science, Northern Virginia Center, Virginia Tech, Falls Church, VA.

[51]  “Informatics as a Platform Supporting Translational Disease Therapeutics and Diagnostics” (July 2006) Asuragen, Inc., Austin, TX.

[52]  “From Systems Biology to Personalized Medicine Informatics: How to Plan for Success” (May 2006) Cincinnati Children's Hospital Medical Center, Cincinnati, OH.

[53]  “Computational Discovery from Large Biological Network Data” (June 2005) Prolexys Pharmaceuticals, Inc., Salt Lake City, UT.

[54]  “A Bioinformatics Study of the Human Protein Interactome” (January 2004) Joslin Diabetes Center, Harvard Medical School, Boston, MA.

[55]  “The Human Protein Interactome: Computational Opportunities and Discovery Surprises” (November 2003) Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA.

[56]  “Computational Proteomics: Mining Hidden Links between Proteins” (November 2003), National Center for Genome Resources, Santa Fe, NM.

[57]  “Extended DBMS: Towards a Bio-computing Platform and a Scientific Discovery Tool” (October 2003) Life Sciences Group, Oracle Corporation, Burlington, MA.

[58]  “Guilt-by-Association: Proteomics Analysis using Random Yeast 2-Hybrid Data” (October 2003) Windber Research Institute, Windber, PA.

[59]  “Knowledge Discovery of High-throughput Protein-protein Interaction Data” (September 2003) Colloquium, Medical Informatics Department, University of Utah, Salt Lake City, UT.

[60]  “Developing a Computational Framework for Mining Yeast-2-hybrid Interaction Data” (August 2002) Myriad Proteomics, Inc., Salt Lake City, UT.

[61]  “Bioinformatics: Managing Biological Data and Discoveries” (April 2002) Monthly Seminar Series, ACM San Francisco Bay Area Local Chapter, Cupertino, CA.

[62]  “Bioinformatics: Challenges, Opportunities, and Transitions” (March 2002) Bay Area Young Scientists Forum, Stanford University, Stanford, CA.

[63]  “Developing Bioinformatics Information Models” (November 2001) Rosetta Inpharmatics, Bothell, WA.

[64]  “A GeneChip Case Study of Discovery-oriented Bioinformatics” (October 2001) Cray-sponsored Computer Science Colloquia, University of Minnesota, Minneapolis, MN.

[65]  “Building Genomic Database Systems for Bioinformatics” (January 2000) Affymetrix, Inc., Santa Clara, CA.

[66]  “Designing A Rat Expression Chip” (March 1999) Affymetrix, Inc., Santa Clara, CA.

[67]  “Experience with a Data-Centric Approach to Building Bioinformatics Systems” (August 1998) Biomedical Informatics Group Seminar, Stanford University, Palo Alto, CA.

Invited Seminars – Indiana Regional (20)

[68]  “Building Connectivity Maps for Drug Re-purposing and Toxicogenomics Studies” (December 2008) Chemical Informatics Division, Eli Lilly and Company, Indianapolis, IN.

[69]  “An Overview of the Lung Cancer ‘Chemo Selection’ Biomarker Development Project” (November 2008) Lung Cancer Working Group, Indiana University Simon Cancer Center, Indianapolis, IN.

[70]  “Systems Biology—Why Bother?” (July 2008) Ground Rounds Seminar, Department of Clinical Pathology, Indiana University School of Medicine, Indianapolis, IN.

[71]  “SysNet: Building Systems Biology Tools towards Predictive, Preventive, and Personalized Biomedical Applications” (April 2008) Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN.

[72]  “GeneTerrain: A Novel Visual Platform for Panel Biomarker Discoveries” (October 2007) Open House, Center for Mathematical Biology & Center for Bio-computing, Indiana University – Purdue University, Indianapolis, IN.

[73]  “Network Biology and Informatics: Bridging Large-scale Biology and Disease-specific Studies” (April 2007) Department of Biology, Purdue University School of Science, Indiana University – Purdue University, Indianapolis, IN.

[74]  “TBD: Computational Systems Biology Agenda 2.0” (April 2007) Integrative Biology Division, Eli Lilly & Company, Greenfield, IN.

[75]  “Overview of Technologies for Predictive Lung Cancer Systems Biology toward Improved Postoperative Survivals” (February 2007) Lung Cancer Working Group, Indiana University Cancer Center, Indianapolis, IN.

[76]  “Computational Systems Biology: New Research Opportunities & Applications” (February 2007) Cyber Center and Department of Computer Science, Purdue University, West Lafayette, IN.

[77]  “Informatics as a Platform Supporting Translational Lung Cancer Research” (June 2006) Lung Cancer Special Interest Group, Indiana University Cancer Center, Indianapolis, IN.

[78]  “Protein Interactions, Networks, and Hubs” (May 2005) Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN.

[79]  “A Few Thoughts on Large Protein Interaction Networks” (March 2005) Round-table Seminar, Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN.

[80]  “Protein-protein Interaction Data: a Global Perspective” (April 2005) Colloquium, Department of Biology, Purdue University School of Science, Indianapolis, IN.

[81]  “Ideas and Tools for Studying Protein Interactomes” (March 2005) Integrative Biology Division, Eli Lilly and Company, Indianapolis, IN.

[82]  “Database Research Opportunities in Bioinformatics” (February 2005) Bioinformatics Colloquium, Indiana University School of Informatics, Indianapolis, IN.

[83]  “Discovery Informatics: A Case Study in System-scale Protein Interactomics Research” (January 2005) Grand Round Seminar Series, Indiana University Cancer Center, Indianapolis, IN.

[84]  “Unraveling Protein Interaction Networks” (December 2004) Colloquium, Biomedical Engineering Department, Purdue University School of Engineering, Indianapolis, IN.

[85]  “Human Protein Interactome: Reasoning on Structures of Randomness” (September 2004) Bioinformatics Colloquium, Department of Statistics, Purdue University, West Lafayette, IN.

[86]  “Collaborative Research Opportunities in Bioinformatics” (April 2004) Indiana University School of Medicine, Indianapolis, IN.

[87]  “The Human Protein Interactome: Initial Survey and Rising Computational Opportunities” (September 2003) Colloquium, Department of Computer and Information Science, Purdue University School of Science, Indianapolis, IN.