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Presentations and Invited Talks

2007

Baird CL, NB Pefaur, SL Servoss, HE Engelmann, KD Miller, RC Zangar, and KD Rodland. 2007. "Selection and Application of scFv Antibodies from Antigen Focused Yeast Surface Display Libraries." Presented by Cheryl Baird (Invited Speaker) at DiPIA, Phoenix, AZ on May 7, 2007. PNNL-SA-55185.

Bandyopadhyay S, MM Matzke, RA Renne, KM Lee, JG Pounds, and KM Waters. 2007. "Integration of Microarray and Proteomic Data with Traditional Toxicity Data Reveals Disease Pathogenesis Pathways in Mouse Model of COPD." Presented by Somnath Bandyopadhyay at Society of Toxicology Annual Meeting, Charlotte, NC on March 27, 2007. PNWD-SA-7763.

Cannon WR, BM Webb-Robertson, DR Baxter, J Laskin, and DJ Taasevigen. 2007. "Advances and Insights from the Use of Physical and Experimental Fragmentation Models for the Identification of Peptides from MS/MS." Presented by William R. Cannon at US HUPO Third Annual Conference, Seattle, WA on March 5, 2007. PNNL-SA-53796.

Cao H, Y Xiong, T Wang, B Chen, TC Squier, and MU Mayer. 2007. "A Red Cy3-Based Biarsenical Fluorescent Probe Targeted to a Complementary Binding Peptide." Presented by Haishi Cao at Protein Society Symposium, Boston, MA on July 22, 2007. PNNL-SA-55113.

Collett J, DS Daly, AM White, and RC Zangar. 2007. "ELISA-BASE and ProMAT: Software extensions for antibody microarray workflow management and prediction of absolute protein concentration within the BioArray Software Environment (BASE 2)." Presented by James R. Collett at US Human Proteome Organization (USHUPO) 3rd Annual Conference, Seattle on March 6, 2007. PNNL-SA-53548.

Gibson TD, KL Schuchardt, EG Stephan, and PR Paulson. 2007. "Semantic Data Grid (SDG) 2nd Provenance Challenge." Presented by Tara Gibson at High-Performance Distributed Computing - Second Provenance Challenge workshop, Monterey, CA on June 26, 2007. PNNL-SA-55994.

Gonzalez RM, SL Servoss, SM Varnum, and RC Zangar. 2007. "Development of a Prescreen to Evaluate Antigen and Antibody Specificity for Use in Multiplex Sandwich ELISA Microarrays." Presented by Rachel M Gonzalez at US HUPO Third Annual Conference, Seattle, WA on March 5, 2007. PNNL-SA-53510.

Jones EM, D Black, JI Shutthanandan, HS Smallwood, MU Mayer, TC Squier, and CA Sacksteder. 2007. "Oxidation-dependent Interactions of Calmodulin with Target Proteins: Implications for the Effects of Oxidative Stress and Ionizing Radiation on Calcium Signaling." Presented by Eric M. Jones at Protein Society 21st Annual Symposium, Boston, MA on July 22, 2007. PNNL-SA-54495.

Karagiosis SA, and NJ Karin. 2007. "Lysophosphatidic Acid Induces Osteocyte Dendrite Outgrowth." Presented by Sue Karagiosis at Amer. Soc. Bone & Mineral Research, Honolulu, HI on September 17, 2007. PNNL-SA-54691.

Karagiosis SA, L Opresko, WB Chrisler, and NJ Karin. 2007. "Molecular Mechanisms of Lysophosphatidic Acid-stimulated Osteoblastic Cell Chemotaxis." Presented by Sue Karagiosis at Amer. Soc. Bone & Mineral Research, Honolulu, HI on September 17, 2007. PNNL-SA-54793.

Karin NJ, KM Waters, R Tan, DS Galileo, and SA Karagiosis. 2007. "Regulation of Bone Cell Function by LPA." Presented by Norm Karin at Federation of American Societies for Experimental Biology (FASEB) conference on lysophosphatidic acid, Tucson, AZ on June 10, 2007. PNNL-SA-55716.

Majors PD, JS Mclean, O Ona, JC Scholten, and RA Wind. 2007. "Hyphenated nuclear magnetic resonance technologies for microbial physiology studies." Presented by Paul Majors (Invited Speaker) at Irish Branch of the Society for General Microbiology Conference, Limerick, Ireland on April 19, 2007. PNNL-SA-55175.

Mclean JS, CL Bilskis, D Saffarini, MF Romine, JK Fredrickson, and AS Beliaev. 2007. "Global Transcriptomic and Physiological Investigations of Cell-Cell Adhesion in Shewanella Reveals Unique Gene Expression Patterns and the Requirement of a Prepillin Peptidase." Presented by Jeffrey Mclean at 2007 American Society for Microbiology General Meeting, Toronto, ON, Canada on May 21, 2007. PNNL-SA-55406.

Pefaur NB, KD Miller, and CL Baird. 2007. "scFv applications in HCV research." Presented by Noah Pefaur (Invited Speaker) at None, San Francisco, CA on March 21, 2007. PNNL-SA-54638.

Reed JL, I Famili, SJ Wiback, CH Schilling, GE Pinchuk, MF Romine, JC Scholten, J Klappenbach, and JK Fredrickson. 2007. "Metabolic Reconstruction of Shewanella oneidensis: A Community Resource." Presented by JCM Scholten (Invited Speaker) at Joint Genomics: GTL Contractor-Grantee Workshop V and Inter-Agency Conference on Metabolic Engineering 2007, Bethesda, MD on February 12, 2007. PNNL-SA-53349.

Regimbal KM, WA De Jong, ER Vorpagel, PT Smith, and GA Anderson. 2007. "Presentation for MSCF Operational Assessment Plan." Presented by Kevin Regimal, Gordon Anderson, Peter Smith, Wibe (Bert) de Jong (Invited Speaker) at Presentation for MSCF Operational Assessment Review, Washington, DC on August 29, 2007. PNNL-SA-56778.

Rodland KD. 2007. "Building a Systems Biology program at PNNL." Presented by Karin D. Rodland (Invited Speaker) at Symposium on Systems Biology, Daejon, Korea, Republic Of on February 7, 2007. PNNL-SA-53802.

Rodland KD. 2007. "Clinical Proteomics: the potential of mass spectrometry." Presented by Karin D. Rodland (Invited Speaker) at Symposium on Systems Biology -- South Korea, Daejon, Korea, Republic Of on February 6, 2007. PNNL-SA-53803.

Rodland KD. 2007. "A Systems Approach to Biomedical Research." Presented by Karin D. Rodland (Invited Speaker) at Seminar at Korea University -- Seoul, Korea, Seoul, Korea, Republic Of on May 3, 2007. PNNL-SA-54907.

Sacksteder CA, JI Shutthanandan, EM Jones, D Black, HS Smallwood, DG Camp, II, W Qian, DJ Bigelow, and TC Squier. 2007. "Unraveling the network of oxidative modifications, protein complexes and cell signaling." Presented by Colette Sacksteder (Invited Speaker) at Integrated Plant Science Retreat, Pullman, WA on February 17, 2007. PNNL-SA-53817.

Scholten JC, MS Lipton, and EJ Ackerman. 2007. "Overcoming the biological barrier to increased hydrogen production by investigating protein complexes involved in reverse electron transport." Presented by Johannes C. Scholten (Invited Speaker) at Society for Industrial Microbiology Annual Meeting , Denver, CO on July 31, 2007. PNNL-SA-56388.

Scholten JC, JL Reed, I Famili, SJ Wiback, GE Pinchuk, MF Romine, MS Lipton, JE Turse, and JK Fredrickson. 2007. "Metabolic flux analyses of Shewanella oneidensis MR-1 central metabolism." Presented by Johannes Scholten at 2007 American Society for Microbiology General Meeting, Toronto, ON, Canada on May 21, 2007. PNNL-SA-55426.

Servoss SL, CL Baird, KD Miller, RC Zangar, DO Apiyo, NB Pefaur, HE Engelmann, and KD Rodland.2007. "Strategies for Improving the Utility of scFv in ELISA Microarrays." Presented by Karin D. Rodland at Gordon Research Conference, Ventura, CA on January 24, 2007. PNNL-SA-53526.

Shankaran H, H Resat, LK Opresko, and HS Wiley. 2007. "Computational and Experimental Insights into the EGFR Signaling Network." Presented by H. Steven Wiley (Invited Speaker) at Engineering Cell Biology — The Cell in Context, Boston, MA on August 6, 2007. PNNL-SA-55771.

Shankaran H, H Resat, L Opresko, and HS Wiley. 2007. "Autocrine Circuits and Feedback Control in EGF Receptor Signaling." Presented by H. Steven Wiley (Invited Speaker) at First q-bio Conference on Cellular Information Processing, Santa Fe, NM on August 11, 2007. PNNL-SA-55871.

Singhal M, and KO Domico. 2007. "CABIN: Collective Analysis of Biological Interaction Networks." Presented by Mudita Singhal at GAGGLE Workshop, Seattle, WA on August 27, 2007. PNNL-SA-56610.

Singhal M, and KO Domico. 2007. "CABIN: Collective Analysis of Biological Interaction Networks." Presented by Mudita Singhal at Shewanella Federation Meeting, Richland, WA on August 15, 2007. PNNL-SA-56611.

Taylor RC, and M Singhal. 2007. "SEBINI (with CABIN) - An Architecture to support systems biology through network inference." Presented by Mudita Singhal, Ronald Taylor (Invited Speaker) at National Cancer Institute, Bethesda, MD on February 23, 2007. PNNL-SA-54206.

Taylor RC. 2007. "SEBINI - an architecture to support systems biology through network inference." Presented by Ronald Taylor (Invited Speaker), Bethesda, MD on February 23, 2007. PNNL-SA-53757.

Taylor RC. 2007. "SEBINI - an architecture to support systems biology through network inference." Presented by Ronald Taylor (Invited Speaker) at NIH proteomics and systems biology interest group meeting, Bethesda, MD on February 15, 2007. PNNL-SA-53776.

Taylor RC. 2007. "SEBINI (with CABIN) - an architecture to support systems biology through network inference." Presented by Ronald Taylor (Invited Speaker) at Argonne National Laboratory, Chicago, IL on April 16, 2007. PNNL-SA-54727.

Taylor RC. 2007. "SEBINI (with CABIN) - an architecture to support systems biology through network inference." Presented by Ronald Taylor (Invited Speaker) at Nothern Univeristy of Illinois, Chicago, IL on April 17, 2007. PNNL-SA-54728.

Taylor RC, AR Shah, CC Treatman, and ML Blevins. 2007. "SEBINI - an architecture to support systems biology through network inference (poster)." Presented by Ronald Taylor at Shewanella Federation meeting, Richland, WA on August 15, 2007. PNNL-SA-56612.

Taylor RC, and M Singhal. 2007. "SEBINI (with CABIN) - an architecture to support systems biology through network inference (poster)." Presented by Ronald Taylor at Gordon Bioinformatics Research Conference, 2007, Andover, NH on June 20, 2007. PNNL-SA-56063.

Taylor RC, and M Singhal. 2007. "SEBINI-CABIN — a software architecture to support systems biology through network inference." Presented by Ronald Taylor (Invited Speaker) at Dana-Farber Cancer Institute, Boston, MA on July 24, 2007. PNNL-SA-56164.

Taylor RC, AR Shah, CC Treatman, and ML Blevins. 2007. "SEBINI - an architecture to support systems biology through network inference (poster)." Presented by Ronald Taylor at Shewanella Federation meeting, Richland, WA on August 15, 2007. PNNL-SA-56612.

Taylor RC, AR Shah, CC Treatman, and ML Blevins. 2007. "SEBINI - an architecture to support systems biology through network inference (poster)." Presented by Ronald Taylor at Gaggle Workshop, Seattle, WA on August 27, 2007. PNNL-SA-56609.

Waters KM. 2007. "Bioinformatics for Systems Biology." Presented by Katrina Waters (Invited Speaker) at PNNL, Richland, WA on March 2, 2007. PNNL-SA-54186.

Waters KM. 2007. "Contribution of Proteomic Data to Networks and Pathways." Presented by Katrina Waters (Invited Speaker) at NCRR Advisory Committee Meeting, Richland, WA on March 14, 2007. PNNL-SA-54323.

Waters KM. 2007. "Bioinformatics Resource Manager: data management for systems biology." Presented by Katrina Waters (Invited Speaker) at Gaggle Workshop 2007, Seattle, WA on August 27, 2007. PNWD-SA-7914.

Waters KM, HS Wiley, and BD Thrall. 2007. "Pathway and network analyses of EGFR signaling from integration of time course microarray and proteomic data." Presented by Katrina Waters (Invited Speaker) at Experimental Biology 2007, Washington, DC on May 2, 2007. PNNL-SA-55108.

Waters KM, LM Masiello, S Bandyopadhyay, JM Jacobs, TJ Weber, R Tan, RD Quesenberry, JG Pounds, and BD Thrall. 2007. "Integration of microarray and proteomic data reveals distinct signaling networks involved in the inflammatory response of RAW 264.7 macrophage cells to lipopolysaccharide and nanoparticle exposure." Presented by Katrina Waters at Gordon Conference on Toxigenomics, New London, NH on June 27, 2007. PNNL-SA-56000.

Waters KM, L Opresko, W Qian, BD Thrall, and HS Wiley. 2007. "Investigating autocrine networks in epithelial cells by integrating proteomics and microarray data." Presented by H. Steven Wiley (Invited Speaker) at Joint BSPR & EBI 2007 Conference, Cambridge, United Kingdom on July 26, 2007. PNNL-SA-55772.

Webb-Robertson BM, and WR Cannon. 2007. "Proteomics Peptide Identification and Visualization." Presented by Bobbie-Jo Webb-Robertson (Invited Speaker) at Demonstration for U Texas San Antonio Health Science Center via Live Meeting, Richland, WA on June 18, 2007. PNNL-SA-55940.

White AM, DS Daly, KK Anderson, and RC Zangar. 2007. "ProMAT: Protein Microarray Analysis Tool." Presented by Amanda White at US HUPO Conference, Seattle, WA on March 7, 2007. PNNL-SA-54214.

Wiley HS. 2007. "Current Research on EGFR Signaling: Translating Systems Biology into Clinically Relevant Information." Presented by H. Steven Wiley (Invited Speaker) at Amgen Global Science Advisory Board Meeting, Philadelphia, PA on February 12, 2007. PNNL-SA-54279.

Wiley HS. 2007. "Autocrine Circuits and Feedback Control in EGF Receptor Signaling." Presented by H. Steven Wiley (Invited Speaker) at LBNL, Berkeley, CA on May 9, 2007. PNNL-SA-55177.

Wiley HS. 2007. "Using a systems approach to understand autocrine signaling and feedback control in the EGF receptor." Presented by H. Steven Wiley (Invited Speaker) at CCSB Seminar Series, Boston, MA on May 3, 2007. PNNL-SA-55178.

Wiley HS. 2007. "Autocrine Circuits and Feedback Control in EGF Receptor Signaling." Presented by H. Steven Wiley (Invited Speaker) at Joint RTK consortium & BSPR & EBI 2007 Workshop: Proteomics and Phosphoproteomics of Receptor Tyrosine Kinase (RTK) Sign, Cambridge, United Kingdom on July 23, 2007. PNNL-SA-55394.

Wiley HS. 2007. "Systems Biology and Cancer." Presented by H. Steven Wiley (Invited Speaker) at ITMAT Symposium, Philadelphia, PA on April 25, 2007. PNNL-SA-54758.

Zangar RC. 2007. "Analytical Methods for Multiplexed ELISA Microarrays." Presented by RC Zangar at HUPO Annual Conference, Seattle, WA on March 5, 2007. PNNL-SA-54096.

2006

Baird CL, MG Warner, KD Miller, AM Pierson, CL Warner, C Bruckner-Lea, and JW Grate. 2006. "Engineered Proteins and Nanomaterials for Biodetection Applications." Presented by Cheryl Baird and Marvin Warner at Chemical and Biological Countermeasure Technologies for Homeland Security Meeting, Boulder, CO on October 10, 2006. PNNL-SA-53551.

Bollinger N, KD Rodland, and HS Wiley. 2006. "Multiple Receptor Subclasses Are Involved in the Transactivation of Epidermal Growth Factor Receptor in Human Mammary Epithelial Cells." Presented by Nikki Bollinger at ASCB, San Diego, CA on December 12, 2006. PNNL-SA-54281.

Lin JT, DL Auberry, BS Hooker, EA Livesay, D Orton, KD Victry, and HS Wiley. 2006. "Proteomics for functional cellular protein complexes: Rapid and direct access to intracellular protein cluster." Presented by Chiann-Tso Lin at ASCB Conference, San Diego, CA on December 12, 2006. PNNL-SA-53138.

McLean JS, and PD Majors. 2006. "In-Situ Monitoring of Metabolism in Environmental and Oral Biofilms." Presented by Jeff Mclean and Paul Majors (Invited Speaker) at Philips Oral Healthcare Meeting, Snoqualmie, WA on December 5, 2006. PNNL-SA-52961.

Oehmen CS, L McCue, JN Adkins, KM Waters, T Carlson, WR Cannon, BM Webb-Robertson, DJ Baxter, ES Peterson, M Singhal, A Shah, and KR Klicker. 2006. "High-Throughput Visual Analytics for Biological Sciences: Turning Data into Knowledge." Presented by Christopher Oehmen (Invited Speaker) at Supercomputing 2006, Tampa, FL on November 14, 2006. PNNL-SA-52705.

Sacksteder CA, W Qian, TV Knyushko, HH Wang, MH Chin, G Lacan, WP Melega, DG Camp, II, RD Smith, DJ Smith, TC Squier, and DJ Bigelow. 2006. "Brain Health: A Potential Link between Tyrosine Nitration and Neurodegenerative Disease." Presented by Colette Sacksteder (Invited Speaker) at Pasco Kennewick Rotary Club, Kennewick, WA on October 11, 2006. PNNL-SA-53549.

Shah A, M Singhal, KR Klicker, and KM Waters. 2006. "A Computational Framework for Systems Biology: The Bioinformatics Resource Manager." Presented by Anuj Shah at Supercomputing 2006, Tampa, FL on November 15, 2006. PNNL-SA-52729.

Singhal M, A Shah, KR Klicker, and KM Waters. 2006. "Enabling data collection, processing, analysis and management - The Bioinformatics Resource Manager." Presented by Mudita Singhal at ASCB (American Society for Cell Biology), San Diego, CA on December 10, 2006. PNNL-SA-53097.

Waters KM. 2006. "Enabling high-throughput data management for systems biology: The Bioinformatics Resource Manager." Presented by Katrina Waters at American Society for Cell Biology Annual Meeting, San Diego, CA on December 10, 2006. PNNL-SA-53099.

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