Publications / Lectures / Posters

2015

Robert Stanley, Jason Eshleman
"Challenges, Risks and Opportunities For
Semantic Interoperability with tranSMART"
Talk at tranSMART Foundation Annual Meeting 2015
Netherlands Cancer Institute, Amsterdam, October 19-21, 2015
Lecture Slides [.pptx, 4.1 MB]

Suzanne Tracy, Robert Stanley, Jason Eshleman, Rodj Martin,
Tom Plasterer, David Brott
"Update on Semantic integration at Astra Zeneca:
SIEVE - Safety Information Evaluation and Visual Exploration"
Presenter: Robert Stanley
Talk at International Semantic Web Conference (ISWC 2015)
Bethlehem, PA October 11-15, 2015
Lecture Slides [.pptx, 5.65MB]

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2014

R. Stanley:
"Semantic Technologies: Real Benefits for Big Data Use Cases"
Talk at SRII Healthcare Analytics Hackathon
Fairmont Hotel, San Jose, CA, April 23-26, 2014
Lecture Slides [.pdf, 6.9 MB]

S. Tracy, S. Furlong, R. Stanley, P. Bogetti, J. Eshleman, M. Goodman:
"Semantic integration at Astra Zeneca:'SIEVE'
Safety Information Evaluation and Visual Exploration"

Talk at Conference on Semantics in Healthcare
and Life Sciences (CSHALS 2014)

Revere Hotel, Boston, MA, February 26-28, 2014
Lecture Slides [.pdf, 3.6 MB]

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2013

R. Stanley:
"Shortest Path to Enriching Your MS Data - and Putting it to Work!"
Stanford Mass Spectrometry Users' Meeting on Mass Spectrometric Applications in Therapeutic Protein Development
Stanford, CA, October 29, 2013
Lecture Slides [.pdf, 4.6 MB]

E. Gombocz:
"Changing the Model in Pharma and Healthcare - Can We Afford to Wait Any Longer?"
9th International Conference Data Integration in Life Sciences (DILS 2013)
Montreal, Canada, July 11-12, 2013
Abstract [.pdf, 0.1 MB]
Proceedings [eBook / Softcover] E.Gombocz in: C.J.O. Baker, G. Butler and I. Jurisica (eds.): 9th International Conference, DILS 2013, Montreal, Canada, July 11-12, 2013, Proceedings Series, LNBI 7970, pp. 1-22, ISBN 978-3-642-39436-2 (2013).

E.A. Gombocz:
"Semantics in a Box: Integrated data appliances to contextualize experiments with a world of knowledge"
Semantic Technology & Business Conference (SemTech 2013)
San Francisco, CA, June 2-5, 2013
Abstract [.pdf, 0.1 MB]
Lecture Slides [.pdf, 12.9 MB]

E.A. Gombocz:
"On the road to production: Semantic integration cases indicate successful adoption to improve knowledge-based decisions in Pharma and healthcare"
NCBO Webinar Series
Stanford, CA, April 19, 2013
Abstract [.html]
Slides [.pdf, 8.6 MB]
WebEx Recording [~ 57 min. stream]

E.A. Gombocz, R.A. Stanley:
"Linked Open Data to Qualify, Enrich and Validate Experiments: The Semantic Approach to Integrated Data is Bearing Fruits"
Poster at CHI's Annual Bio-IT World Conference & Expo
(Bio-IT 2013)

World Trade Center, Boston, MA, April 9-11, 2013
Abstract [.pdf, 0.2 MB]
Poster (portrait) [.pdf, 2.0 MB]

E.A. Gombocz, A. Splendiani, M.A. Musen, R.A. Stanley, J.A. Eshleman:
"Yes, we can! Lessons from Using Linked Open Data (LOD) and Public Ontologies to Contextualize and Enrich Experimental Data"
Talk and Poster #5 at Conference on Semantics in Healthcare
and Life Sciences (CSHALS 2013)

Royal Sonesta Hotel, Cambridge, MA, February 27-March 1, 2013
Abstract [.pdf, 0.1 MB]
Lecture Slides (4:3) [.pdf, 4.7 MB]
Poster (squared) [.pdf, 1.2 MB]
ePoster (landscape, 16:9) [.pdf, 1.1 MB]

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2012

E. Gombocz, J. Candlin:
"How semantic technology helps fighting infectious diseases: Biological systems approach to understand microbial pathogens"
Talk at Semantic Technology & Businesss Conference
(SemTech 2012)

Hilton Union Square, San Francisco, CA, June 3-7, 2012
Abstract [.pdf, 0.1 MB]
Lecture Slides [.pdf, 5.4 MB]

E. Gombocz:
"From Individual Experiments to Informed Decision Making: Challenges, Sucess Stories and Opportunities in Collaborative Science"
Seminar and Panel Discussion about
Data for Decision Making: Lab, Enterprise, Web
(Center for Computing for Life Sciences Seminars)

SFSU CCLS Science Bld. (SCI), San Francisco, CA, May 3, 2012
Seminar Slides [.pdf, 6.4 MB]

E. Gombocz, J. Candlin, R. Stanley, D. Chiang:
"Semantically Enhancing Protein Identification: Systems Biology Knowledgebase for Infectious Disease Screening"
Poster at CHI's 10th Annual Bio-IT World Conference & Expo
(Bio-IT 2012)

World Trade Center, Boston, MA, April 24-26, 2012
Abstract [.pdf, 0.1 MB]
Poster (portrait) [.pdf, 1.0 MB]

E. Gombocz, J. Candlin:
"Semantic Integration to Characterize Microbial Pathogens: Multi-Resource Enrichment of Experimental Proteomic and Genomic Datasets"
Poster at Conference on Semantics in Healthcare and Life Sciences (CSHALS 2012)
Royal Sonesta, Cambridge, MA, February 22-24, 2012
Abstract [.pdf, 0.1 MB]
Poster (squared) [.pdf, 1.1 MB]

E. Gombocz, J. Candlin:
"A Novel Approach to Recognize Peptide Functions in Microorganisms: Establishing Systems Biology-based Relationship Networks to Better Understand Disease Causes and Prevention "
Lecture at 8th Annual Conference US Human Proteome Organisation: The Future of Proteomics (HUPO 2012)
Palace Hotel, San Francisco, CA, March 4-7, 2012
Abstract [.pdf, 0.1 MB]
Lecture Slides [.pdf, 4.6 MB]

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2011

R. Stanley:
"Semantic Technologies in Practice: Transforming the Field by Taking the Pain out of Data Integration"
Lecture at Semantic Technology 2011 (SemTech)
Hilton, San Francisco, CA, June 5-9, 2011
Abstract [.pdf, 0.4 MB]
Lecture slides [.pdf, 1.9 MB]

R. Stanley:
"Resource Description Framework Approach to Data Publication and Federation"
Presentation to Pistoia Alliance Technical Committee and Invited Attendees, San Francisco, CA, June 6, 2011
Lecture Slides [.pdf / 1.4 MB]
Recording [.html / 14 min.]

E. Gombocz:
"Semantic cross-domain integration: The intersection of research, public, and clinical data; creating applicable knowledge for decision support in patient-centric healthcare"
NCBO Webinar Series Stanford, CA, May 4, 2011
Abstract [.html]
Lecture Slides [.pdf / 3.2 MB]
WebEx Recording [~54 min. stream]

T.N. Plasterer, R. Stanley, E. Gombocz:
"Correlation Network Analysis and Knowledge Integration"
In: "Applied Statistics for Network Biology: Methods in Systems Biology", M. Dehmer, F. Emmert-Streib, A. Graber, A. Salvador (Eds.)
Wiley-VCH, Weinheim, ISBN: 978-3-527-32750-8 (2011)

E. Gombocz, R. Stanley, J. Eshleman, C. Rockey:
"Semantic Data Integration: Answer to Complexity in Translational Research"
Poster at CHI's Bio-IT World Conference 2011
World Trade Center, Boston, MA, April 12-14, 2011
Abstract [.pdf / 0.1 MB]
Poster (portrait) [.pdf / 1.0 MB]

R. Stanley, B. McManus, R. Ng, E. Gombocz, J. Eshleman, C. Rockey:
"Case Study: Applied Semantic Knowledgebase for Detection of Patients at Risk of Organ Failure through Immune Rejection"
Joint Case Study of IO Informatics and University British Columbia (UBC), NCE CECR PROOF Centre of Excellence, James Hogg iCAPTURE Centre, Vancouver, BC, Canada, March 29, 2011
W3C Semantic Web Use Cases and Case Studies

K. Qaadri:
"Knowledge building environments"
Lecture at Best Practices for Personalized Medicine (B2PM 2011)
Session I: Creating Knowledge, Applying Knowledge
Sheraton Vancouver Wall Centre, Vancouver, BC, Canada, March 8-9, 2011
Lecture Slides [.pdf / 3.7 MB]

E. Gombocz:
"ASK for confident decisions: Harnessing the power of semantics"
Lecture at Best Practices for Personalized Medicine (B2PM 2011)
Session VIII: Delivering Personalized Care
Sheraton Vancouver Wall Centre, Vancouver, BC, Canada, March 8-9, 2011
Lecture Slides [.pdf / 3.7 MB]

E. Gombocz, D. Milward, J. Eshleman:
"Contextual understanding of experimental data via formal semantic integration of NLP-extracted content with other semantically integrated resources"
Joint Poster of IO Informatics and Linguamatics at Conference on Semantics in Healthcare and Life Sciences (CSHALS 2011)
Royal Sonesta Hotel Boston, Cambridge, MA, February 23-25, 2011
Poster (portrait) [.pdf / 0.8 MB]

C. Rockey:
"A 'Killer App' for Semantic Technologies: Point-and-Click Data Integration Tools Make it Easy to Deliver Targeted Semantic Knowledge Bases"
Tech Talk at Conference on Semantics in Healthcare and Life Sciences (CSHALS 2011)
Royal Sonesta Hotel Boston, Cambridge, MA, February 25, 2011
Abstract [.pdf / 0.3 MB]

E. Gombocz, R. Stanley:
"Predictive Toxicology: Applied Semantics with a major impact on drug safety"
Poster at FDA's Drug Safety Workshop: Pharmacological Mechanism-Based Drug Safety Assessment and Prediction
FDA, White Oak Campus, Silver Spring, MD, January 27-28, 2011
Poster (portrait) [.pdf / 1.1 MB]

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2010

E. Gombocz, R. Stanley, J. Eshleman:
"Computational R&D in Action: Integrating Correlation and Knowledge Networks For Treatment Response Modeling and Decision Support"
Poster at Advanced Strategies for Computational Drug R&D
Park Plaza Hotel, Boston, MA, Sept. 28-Oct. 1, 2010
Abstract [.pdf / 0.6 MB]
Poster (portrait) [.pdf / 1.6 MB]

R.T. Ng, E. Gombocz:
"Biomarker Development to Improve Decision Support for the Treatment of Organ Failures: How Far Are We Today?"
Joint Lecture at CHI's ADAPT 2010
Hyatt Regency Crystal City, Arlington, VA, Sept. 13-16, 2010
Lecture Slides [.pdf / 4.1 MB]

J. Eshleman, E. Gombocz, R. Stanley:
"Personalized Medicine in Action: Screening with Semantic Biology Models from Integrated Data Correlation and Knowledge Networks"
Poster at CHI's ADAPT 2010
Hyatt Regency Crystal City, Arlington, VA, Sept. 13-16, 2010
Poster (portrait) [.pdf / 1.6 MB]

E. Gombocz:
"The New Information Age in Life Sciences and Clinics: From Static Data Warehouses to Decision Support based on Dynamic Semantically Integrated Data and Knowledge Networks"
Keynote Lecture at BIT's 2nd Annual World Congress BioSoft 2010
World Exposition Center, Dalian, China, June 23-25, 2010
Abstract [.pdf / 270 KB]
Lecture Slides [.pdf / 7.6 MB]

R. Stanley, E. Gombocz, J. Eshleman, C. Rockey:
"From Concepts to Production: Semantic Technology Solves Real Life Sciences and Healthcare Challenges"
Poster at Semantic Technology 2010 (SemTech)
Hilton, San Francisco, CA, June 21-25, 2010
Poster (portrait) [.pdf / 1.1 MB]

E.A. Gombocz:
"Research Data Integration of Retrospective Studies for Prediction of Disease Progression"
IO Informatics, Berkeley, CA, June 2010
White Paper [.pdf / 1.8 MB]

E. Gombocz, R. Stanley, J. Eshleman, Z. Rhoades:
"From multiple biomarkers to patient-centric personalized medicine: An 'Applied Semantic Knowledgebase' for decision support"
Poster at CHI's Biomarker World Congress 2010
Loews, Philadelphia, PA, May 4-6, 2010
Poster (portrait) [.pdf / 1 MB]

Z. Rhoades, E. Gombocz:
"Semantic Integration and Modeling of Scientific Data Sources"
IO Informatics, Berkeley, CA, May 2010
White Paper [.pdf / 1.4 MB]

E. Gombocz, R. Stanley, Z. Rhoades, J. Eshleman:
"Applied Semantic Knowledgebases (ASK ): Confident decisions in personalized medicine using semantic biology models"
Poster at CHI's Bio-IT World Conference 2010
World Trade Center, Boston, MA, April 20-22, 2010
Poster (portrait) [.pdf / 1.0 MB]

Z. Rhoades, E.A. Gombocz:
"Charting the Unknown: Capturing and Delivering Value From Understanding Complex Biological Responses"
Am. Biotechnology Laboratory 28 (3): (2010).

E.A. Gombocz:
"Predictive models for biology in personalized medicine: Are we there yet? "
Lecture at Conference on Semantics in Healthcare and Life Sciences (CSHALS)
Royal Sonesta Hotel Boston, Cambridge, MA, February 24-26, 2010
Lecture slides [.pdf / 3.9 MB]

R.A. Stanley, E.A. Gombocz, Z. Rhoades:
"Realizing personalized medicine with semantic technology: Applied Semantic Knowledgebases (ASK ) at work"
Poster at Conference on Semantics in Healthcare and Life Sciences (CSHALS)
Royal Sonesta Hotel Boston, Cambridge, MA, February 24-26, 2010
Poster (portrait)[.pdf / 1.4 MB]

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2009

E.A. Gombocz:
"Changing decision-making in life sciences & personalized medicine: Applied Semantic Knowledgebases (ASK ) at work!"
Lecture at Planet Connect Life Science Symposium: Advances Towards Personalized Medicine
Claremont Resort and Spa, Berkeley, CA, November 19, 2009
Abstract

R.A. Stanley, Z. Rhoades, E.A. Gombocz:
"Applied Semantic Knowledgebases (ASK): Changing how knowledge is built and applied in Life Sciences and personalized medicine"
Poster at Adapt 2009 Accelerating Development & Advancing Personalized Therapy
Grand Hyatt Washington, Washington DC, September 22-25, 2009
Poster (portrait) [.pdf / 1.1 MB]

R. Stanley:
"NIST / CLDA Case Study: From Data Management, Exploration and Analysis to Applied Combinatorial Biomarkers for Hepatotoxicity"
Lecture at GTC Bio 3rd Annual Biomarker Discovery and Development
San Diego, CA, July 10-11,2009
Lecture slides [.pdf / 6.5 MB]

E.A. Gombocz, Z. Rhoades:
"Predictive Toxicology: Applied Semantics with major implications towards safer drugs"
Poster at SemTech 2009 Semantics Technology Conference
The Fairmont Hotel, San Jose, CA, June 14-18, 2009
Poster (portrait) [.pdf / 1.3 MB]

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2008

E.A. Gombocz, A.J. Higgins, P. Hurban, E.K. Lobenhofer, F.T. Crews, R.A. Stanley, C. Rockey, T. Nishimura:
"Does network analysis of integrated data help understanding how alcohol affects biological functions?" - Results of a semantic approach to biomarker discovery
Poster at CHI's Biomarker Discovery Summit 2008 at Loews Philadelphia Hotel, Philadelphia, PA, September 29-October 1, 2008
Poster (portrait) [.pdf / 1.6 MB]

E.A. Gombocz, R.A. Stanley, Toshiro Nishimura, Chuck Rockey:
"From genes, proteins, metabolites, tissue analytics and literature towards a coherent knowledgebase: Semantics at work"
Poster at CHI's Beyond Genome 2008 at Fairmont Hotel, San Francisco, CA, June 8-12, 2008
Poster (portrait) [.pdf / 1.0 MB]

M. Wilkinson:
"Focus biomarker qualification: Semantic applications for translational medicine and their applicability for industry, clinics and academic centers of excellence - REPORT FROM THE WORKING GROUP"
Lecture at CHI's Biomarker World Congress 2008 at Loews Philadelphia Hotel, Philadelphia, PA, May 19-21, 2008
Lecture slides [.pdf / 8.2 MB]

E.A. Gombocz, Toshiro Nishimura, Chuck Rockey:
"Towards better understanding of complex biology: Ontology merging across data sources using multiple thesauri in semantic networks"
Poster at CHI's Biomarker World Congress 2008 at Loews Philadelphia Hotel, Philadelphia, PA, May 19-21, 2008
Poster (portrait) [.pdf / 1.0 MB]

E.A. Gombocz, R.A. Stanley, T. Nishimura, A.J. Higgins, P. Hurban:
"From observations to understanding: A semantic systems biology approach for biomarker discovery in translational medicine"
Poster at CHI's Biomarker World Congress 2008 at Loews Philadelphia Hotel, Philadelphia, PA, May 19-21, 2008
Poster (portrait) [.pdf / 0.8 MB]

A.J. Higgins, E.A. Gombocz, R.A. Stanley:
"From Correlation to Biological Understanding: Multi-modal semantic networks for biomarker discovery and qualification"
Lecture at CHI's Bio-IT World 2008 at World Trade Center,
Boston, MA, April 28-30, 2008
Lecture slides [.pdf / 8.6 MB]

E.A. Gombocz, R.A. Stanley, C. Rockey, T. Nishimura:
"Data integration framework for discovery and validation: Smart merging of experimental and public data across ontologies and taxonomies"
Poster at CHI's Bio-IT World 2008 at World Trade Center,
Boston, MA, April 28-30, 2008
Poster (portrait) [.pdf / 0.9 MB]

T. Slater, J.S. Almeida, M. Wilkinson, A.J. Higgins, E.A. Gombocz,
T. Nishimura:
"Working Group on Semantic Applications in Translational Research: Industry and academic centers of excellence join forces to build coherent networks to comprehend complex biological systems in context of personalized medicine and rational drug design"
Poster at CHI's Molecular Medicine Tri-Conference 2008 at Moscone North Convention Center,
San Francisco, CA, March 26-27, 2008
Poster (portrait) [.pdf / 1.1 MB]

E.A. Gombocz, A.J. Higgins, R.A. Stanley:
"Using semantics in biomarker discovery: Unified cross-OMICS correlation networks help scientists understanding biological functions"
Poster at CHI's Molecular Medicine Tri-Conference 2008 at Moscone North Convention Center,
San Francisco, CA, March 26-27, 2008
Poster (portrait) [.pdf / 1.5 MB]

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2007

E. Gombocz, R. Stanley:
"Processing, Annotating, and Searching; Interacting Efficiently With any Image"
Am. Biotechnology Laboratory 25 (10): (2007). [.pdf / 8.4 MB]

A. Higgins:
"Discovery of Toxicity Biomarkers through Application of Correlation Networks and Canonical Pathways"
Lecture at CHI's Biomarker Discovery Summit: Bridging the Silos in Biomarker Discovery and Validation at Loews Philadelphia Hotel, Philadelphia, PA, September 17-19, 2007
Lecture slides [.pdf / 10.2 MB]

E. Gombocz, A. Higgins:
"Discovery and Validation of Toxicity Biomarkers through Application of Correlation Networks and Canonical Pathways"
Lecture at GTCbio's Rediscovering Biomarkers: Detection, Development, and Validation at San Diego Marriot La Jolla, San Diego, CA, July 23-24, 2007
Lecture slides [.pdf / 4.5 MB]

E.Gombocz, A. Higgins:
"Discovery and Validation of Toxicity Biomarkers Using Correlation Networks and Canonical Pathways"
Poster at CHI's 8th Annual Beyond Genome at Fairmont Hotel,
San Francisco, CA, June 21-22, 2007
Poster (portrait) [.pdf / 1.2 MB]

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2006

E.Gombocz, R. Stanley, M. Travers:
"From disparate multi-disciplinary data to coherent knowledge: Informatics for systems biology-based disease profiling"
Lecture at HUPO 2006 at Long Beach Conference Center, Long Beach, CA, October 28 - November 1, 2006
Molecular & Cellular Proteomics 5 (10): S17 (2006)
[Abstract 93]

Lecture slides [.pdf / 6.0 MB]

R.Stanley, E.Gombocz:
"Translational Informatics for Systems Biology"
Am. Biotechnol. Laboratory 24 (7): p.24 - 26 (2006).

R.Stanley:
"A Case Study for Integration Informatics: From Data Integration and Management to Marker-based Diagnostic Models"
Lecture at CHI's Beyond Genome 2006 at the Fairmont, San Francisco, CA, June 19-21 , 2006
Lecture slides [.pdf / 3.2 MB]

E.A. Gombocz, R.A. Stanley, M. Travers:
"Translational Informatics Applied To Systems Biology: From Data Integration and Process Management to Diagnostics Models "
Poster at the QB3 Biomedical Engineering Symposium at the University of California San Francisco, San Francisco CA, April 26, 2006
Poster (portrait) [.pdf / 1.0 MB]

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2005

E.A. Gombocz, R.A. Stanley:
"Intelligent data: Towards systems biology for proteomics in a single system"
Poster at the 4th Annual World Congress of the Human Proteome Organization [HUPO] at the International Congress Center in Munich, Germany, August 28-September 1, 2005
Poster (portrait) [.pdf / 1.0 MB]

E.A. Gombocz, R.A. Stanley:
"Achieving interoperability in Systems Biology: New informatics methods for user-centric, lightweight integration of heterogeneous data" Poster at the 4th International Symposium on Challenges in Systems Biology at the Institute for Systems Biology in Seattle, WA, April 24-25, 2005
Abstract [.pdf / 1.5 MB]

E.Gombocz, R.Stanley:
"Bringing Life Sciences together: Lightweight, regulatory-compliant knowledge management across heterogeneous data sources" Workshop at the 229th ACS National Meeting in San Diego, CA, March 13 -17, 2005
Abstract [.pdf / 69 kB]

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2004

E.Gombocz:
" Beyond LIMS: Next Level of Scientific Information Integration and 2DE Analysis" Presentation and workshop at 21st Annual AES/AIChE Meeting Nov. 7-12, 2004 in Austin, TX
Abstract [.pdf / 531 kB]
Poster (landscape) [.pdf / 2.3 MB]

E.A. Gombocz, R.A. Stanley, R.L. Stevenson:
"From Acquisition to Identification Using Global Data Resources: Fast, Comprehensive Knowledge Building in 2-D Electrophoresis" Presentation at Lab Automation 2004 Jan.31-Feb.5, 2004 in San Jose, CA
Abstract [.pdf / 95 kB]

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2003

E.Gombocz, R.Stanley:
"2DE as Part of Integrated Proteomics: A Full System's Biology Approach" Presentation at 20th Annual AES/AIChE Meeting Nov.16-21, 2003 in San Francisco, CA
Poster (portrait) [.pdf / 626 kB]
Poster (landscape) [.pdf / 674 kB]
Full paper[.pdf / 3.2 MB]

E.Gombocz:
"From the Early Days of Automated Electrophoresis with in-Gel Assaying and Elution to New Avenues in Integrated Multidimensional Bioinformatics and Computational Biology using Intelligent Data" International NIH Workshop 'Electrophoretic Separations in Biology and Medicine: past and Future. Honoring Andreas Chrambach for 40 Years Achievements in Science', National Institutes of Health, Bethesda, MD, June 5, 2003 (2003).

R.A. Stanley, W.S. Hancock:
"Bioinformatics in the Clinic - Challenges And Opportunities For Improved Trials And Clinical Care"
Am. Biology Laboratory 3 (3): p 29-36 (2003).

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2002

W.S. Hancock, S.L. Wu, R.A. Stanley, E.A. Gombocz:
"Publishing Large Proteome Dataset: Scientific Policy Meets Emerging Technologies"
Trends in Biotechnology 20 (12) (Suppl.) S34-S44 (2002).

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