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Workshops
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Oral Presentations
Abstracts/Posters

Workshops
NIH Proteomics Workshop, April 2008
Schedule & Contacts
Protein sequence analysis by Raja Mazumder
Sequence-based analyses by Lai-Su Yeh
Bioinformatics resources by ZhangZhi Hu
Proteomics and protein bioinformatics - Overview by Anastasia Nikolskaya
NIH Proteomics Workshop, March 2007
Schedule & Contacts
Protein Sequence Analysis - Overview by Raja Mazumder
Tutorial: Bioinformatics Resources by Zhang-Zhi Hu
Sequence Based Analysis Tutorial by Lai-Su Yeh
Functional Analysis of Protein Sequences: Annotation and Family Classification by Anastasia Nikolskaya
NIH Proteomics Workshop, October 2006
Schedule & Contacts
Overview: Protein Sequence Analysis by Darren Natale
Tutorial: Bioinformatics Resources by Zhang-Zhi Hu
Tutorial: Sequence-Based Analysis by Cecilia Arighi
Functional Analysis of Protein Sequences: Annotation and Family Classification by Anastasia Nikolskaya
NIH Proteomics Workshop, March 2006
Schedule & Contacts
Overview: Protein Sequence Analysis by Raja Mazumder
Tutorial: Bioinformatics Resources by ZhangZhi Hu
Tutorial: Sequence-Based Analysis by Lai-Su Yeh
Overview: Proteomics and Protein Bioinformatics by Anastasia Nikolskaya
NIH Proteomics Workshop, October 2005
Schedule & Contacts
Overview: Protein Sequence Analysis by Raja Mazumder
Tutorial: Bioinformatics Resources by Zhang-Zhi Hu
Tutorial: Sequence-Based Analysis by Lai-Su Yeh
Overview: Proteomics and Protein Bioinformatics by Anastasia Nikolskaya
NIH Proteomics Workshop, March 2005
Schedule & Contacts
Overview: Protein Sequence Analysis by Raja Mazumder
Tutorial: Bioinformatics Resources by ZhangZhi Hu
Tutorial: Sequence-Based Analysis by Lai-Su Yeh
Overview: Proteomics and Protein Bioinformatics by Anastasia Nikolskaya
NIH Proteomics Workshop, March 2004
Schedule & Contacts
Overview: Protein Sequence Analysis by Raja Mazumder
Tutorial: Bioinformatics Resources by ZhangZhi Hu
Tutorial: Sequence-Based Analysis by Lai-Su Yeh   Test Sequence
Overview: Proteomics and Protein Bioinformatics by Anastasia Nikolskaya
NIH Proteomics Workshop, October 2003
Schedule & Contacts
From Protein Sequence to Function: Functional Analysis of Protein Sequences and Protein Classification by Anastasia Nikolskaya
Demo: Protein Information Resource by Raja Mazumder
Tutorial: Bioinformatics Resources by ZhangZhi Hu
NIH Proteomics Workshop, March 2003
Schedule & Contacts
Bioinformatics and Proteomics by Anastasia Nikolskaya
Demo: Protein Information Resource by Lai-Su Yeh
Tutorial: Bioinformatics Resources by ZhangZhi Hu

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Oral Presentations
Protein Bioinformatics Advances and Challenges
Sona Vasudevan and Peter McGarvey
Presented at Georgetown University Medical Center, May 15, 2007
Presentation
Framework for a Protein Ontology
Darren Natale
Presented at the ACM First International Workshop on Text Mining in Bioinformatics (TMBIO 2006), which is part of the ACM Fifteenth Conference on Information and Knowledge Management (CIKM), Arlington, VA, November 10, 2006
Presentation
Bioinformatics at NIAID Biodefense Proteomics Administrative Resource Center
McGarvey P. and Wu CH.
Presented at the 4th Annual World Congress of Human Proteome Organization (HUPO-2005), Munich, Germany, 2005
Abstract Presentation
PIR: A Comprehensive Resource for Functional Analysis of Protein Sequences and Families
Anastasia Nikolskaya/ Lai-Su Yeh
13th Annual International Conference on Intelligence Systems for Molecular Biology, Detroit, MI, June 26-29, 2005
Abstract
caBIG Grid-Enablement of PIR/UniProt Data Source
Baris Suzek
International Symposium on Web Services for Computational Biology and Bioinformatics , Blacksburg, VA, May 26-27, 2005
Abstract
The PIRSF Protein Classification System as a Basis for Automated UniProt Protein Annotation
Darren Natale
2nd annual International Conference on Bioinformatics and Computational Biology (Icobicobi), Angra dos Reis in Brazil, October 25-28, 2004
Abstract Presentation
Complementing Gene Ontology with PIRSF Classification-based Protein Ontology
Anastasia Nikolskaya
Standards and Ontologies For Functional Genomics (SOFG) Conference, Philadelphia, PA, October 23-26, 2004
Presentation
PIRSF Protein Classification System And Sequence Annotation
Anastasia Nikolskaya
21th Mid-Atlantic Plant Molecular Biology Society Conference (MAPMBS 2004), Laurel, MD, August 19-20, 2004
Presentation
PIRSF Protein Classification System
Raja Mazumder
ISMB/ECCB Conference, Glasgow, UK, July 31-August 4, 2004
Abstract

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Abstracts/Poster Presentations
Potential 2-Aminosuccinimide Structures in Mollusc Proteins
J.S. Garavelli and M. Hirshberg
Protein Sci. (13) (suppl.) abstract 196, 2012.
Poster
Framework For A Protein Ontology
Darren A. Natale, Cecilia N. Arighi, Lai-Su L. Yeh, Winona C. Barker, Judith Blake, Ti-Cheng Chang, Zhangzhi Hu, Hongfang Liu, Barry Smith, and Cathy H. Wu
Presented at caBIG Annual Meeting, Washington D.C., February 5-7, 2007.
Poster
gridPIR: A central resource for genomic and proteomic information
Baris E. Suzek, Hongzhan Huang, Hsing-Kuo Hua, Peter McGarvey, Cathy H. Wu
Presented at caBIG Annual Meeting, Washington D.C., February 5-7, 2007.
Poster
Science Gateway for Protein Analysis on the TeraGrid
Leslie Arminski, Hongzhan Huang, Peter McGarvey, Baris Suzek, Cathy Wu
Presented at caBIG Annual Meeting, Washington D.C., February 5-7, 2007.
Poster
Object Modeling for Semantic Meaning
Baris E. Suzek, Hongzhan Huang, Hsing-Kuo Hua, Peter McGarvey, Cathy H. Wu
Presented at caBIG Annual Meeting, Washington D.C., February 5-7, 2007.
Poster
PIRSF Protein Family Classification System
Anastasia Nikolskaya, Cecilia Arighi, Winona Barker, Hongzhan Huang, Raja Mazumder, Darren Natale, Sona Vasudevan, C.R. Vinayaka, Lai-Su Yeh, Cathy Wu
Presented at the Plant and Animal Genome XV Conference, San Diego, California, January 13-17, 2007.
Poster
Framework For A Protein Ontology
Lai-Su L. Yeh, Darren A. Natale, Cecilia N. Arighi, Winona C. Barker, Judith Blake, Ti-Cheng Chang, Zhangzhi Hu, Hongfang Liu, Barry Smith, and Cathy H. Wu
Presented at the Plant and Animal Genome XV Conference, San Diego, California, January 13-17, 2007.
Poster
The PIRSF system for protein classification, rule-based annotation, and ontology mapping
Darren A. Natale, Cecilia Arighi, Winona Barker, Zhangzhi Hu, Hongzhan Huang, Robel Kahsay, Raja Mazumder, Anastasia Nikolskaya, Sona Vasudevan, C. R. Vinayaka, Lai-Su Yeh, and Cathy H. Wu
Presented at the 14th Annual International Conference on Intelligent Systems for Molecular Biology, Fortaleza, Brazil, August 6-10, 2006.
Abstract
Best Poster Award- Prediction of catalytic residues in proteins using machine learning techniques
Petrova N and Wu CH
Presented at the Computational Systems Bioinformatics conference (CSB2006), Stanford University, California, August 14-18, 2006.
Abstract Poster
The UniProt Consortium
The UniProt Consortium
Presented at the In-Silico Analysis of Proteins Celebrating the 20th anniversary of Swiss-Prot Meeting, Fortaleza, Brazil, July 30-August 04, 2006.
Poster
RLIMS-P: A Rule-Based Literature Mining System for Protein Phosphorylation
Hu ZZ, Yuan X, Torii M, Vijay-Shanker K, and Wu CH
Presented at the In-Silico Analysis of Proteins Celebrating the 20th anniversary of Swiss-Prot Meeting, Fortaleza, Brazil, July 30-August 04, 2006.
Poster
NIAID-Biodefense Proteomics Research Programs
Peter McGarvey, Raja Mazumder, Hongzhan Huang, Jian Zhang and Cathy Wu
Presented at the In-Silico Analysis of Proteins Celebrating the 20th anniversary of Swiss-Prot Meeting, Fortaleza, Brazil, July 30-August 04, 2006.
Poster
The iProXpress Knowledge System for Proteomic Data Analysis
Hongzhan Huang, Zhang-Zhi Hu, Peter McGarvey and Cathy H. Wu
Presented at the In-Silico Analysis of Proteins Celebrating the 20th anniversary of Swiss-Prot Meeting, Fortaleza, Brazil, July 30-August 04, 2006.
Poster
iProLINK – A Literature Mining Resource at PIR (integrated Protein Literature INformation and Knowledge )
Hu ZZ, Liu H, Vijay-Shanker K, Mani I, and Wu CH
Presented at the In-Silico Analysis of Proteins Celebrating the 20th anniversary of Swiss-Prot Meeting, Fortaleza, Brazil, July 30-August 04, 2006.
Poster
Protein Information Resource
Protein Information Resource
Presented at the In-Silico Analysis of Proteins Celebrating the 20th anniversary of Swiss-Prot Meeting, Fortaleza, Brazil, July 30-August 04, 2006.
Poster
Prediction of catalytic residues in proteins using machine learning techniques
Natalia Petrova and Cathy Wu
Presented at the In-Silico Analysis of Proteins Celebrating the 20th anniversary of Swiss-Prot Meeting, Fortaleza, Brazil, July 30-August 04, 2006.
Poster
PIR and caBIG
Baris E. Suzek, Hongzhan Huang, Hsing-Kuo Hua, Peter McGarvey and Cathy H. Wu
Presented at the In-Silico Analysis of Proteins Celebrating the 20th anniversary of Swiss-Prot Meeting, Fortaleza, Brazil, July 30-August 04, 2006.
Poster
CUPID: Core and Unique Protein IDentification
Raja Mazumder and Darren Natale
Presented at the In-Silico Analysis of Proteins Celebrating the 20th anniversary of Swiss-Prot Meeting, Fortaleza, Brazil, July 30-August 04, 2006.
Poster
UniProt Non-redundant Reference Cluster (UniRef) Databases
UniProt Consortium
Presented at the In-Silico Analysis of Proteins Celebrating the 20th anniversary of Swiss-Prot Meeting, Fortaleza, Brazil, July 30-August 04, 2006.
Poster
The PIRSF Protein Classification System as a Basis for Automated UniProtKB Protein Annotation
Protein Information Resource
Presented at the In-Silico Analysis of Proteins Celebrating the 20th anniversary of Swiss-Prot Meeting, Fortaleza, Brazil, July 30-August 04, 2006.
Poster
Grid-Enablement of Protein Information Resource (gridPIR)
Baris E. Suzek, Hongzhan Huang, Scott Chung, Hsing-Kuo Hua, Peter McGarvey, Cathy H. Wu
Presented at the caBIG Annual Meeting, Arlington, VA, April 9-11, 2006.
Poster
The iProXpress Knowledge System for Proteomic Data Analysis
Zhang-Zhi Hu, Hongzhan Huang, Peter McGarvey, An Chi, Julio Valencia, Cathy H. Wu
Presented at US HUPO Annual Conference 2006, Boston, MA, 2006.
Abstract Poster
Protein Information Resource (PIR): An integrated bioinformatics resource for functional proteomics
McGarvey P, Hu Z.Z and Wu, C.H.
Presented at the 1st U.S. HUPO Annual Symposium, Washington, DC, 2005.
Abstract

Web Services for PIR/UniProt Databases
Baris E. Suzek, Hongzhan Huang, Scott Chung, Hsing-Kuo Hua, Peter McGarvey, Zhangzhi Hu, Cathy Wu
Presented at the 13th Annual International Conference on Intelligence Systems for Molecular Biology, Detroit, MI, 2005.

Abstract

Literature Data Mining and Protein Ontology Development at the Protein Information Resource (PIR)
Hu ZZ, Mani I, Liu H, Hermoso V, Fang C, Vijay-Shanker K, Nikolskaya A, Natale DA, and Wu CH
Presented at the 13th Annual International Conference on Intelligence Systems for Molecular Biology, Detroit, MI, 2005.

Abstract Poster

UniProt: the Universal Protein Resource
L.S. Yeh, UniProt Consortium
Presented at the 13th Annual International Conference on Intelligence Systems for Molecular Biology, Detroit, MI, 2005.

Abstract Poster

PIRSF Protein Family Classification System
Anastasia Nikolskaya, Sehee Chung, Hongzhan Huang, Raja Mazumder, Darren Natale, Lai-Su Yeh, Cathy H. Wu
Presented at the 13th Annual International Conference on Intelligence Systems for Molecular Biology, Detroit, 2005

Abstract Poster

Prediction of catalytic residues in proteins using machine-learning techniques
Natalia V. Petrova, Cathy H. Wu
Presented at the 13th Annual International Conference on Intelligence Systems for Molecular Biology, Detroit, 2005

Abstract
PIR Non-Redundant Reference Protein Database (PIR-NREF)
Baris Suzek
Sixth Annual International Conference on Research in Computational Molecular Biology, April 18-27, 2002, Washington, D.C.
Superfamily System for Functional Classification of Protein Sequences: Recognizing Cellular Phosphoesterases in Sequenced Genomes
W. C. Barker, H. Huang, L.S. Yeh, and C.H. Wu
Presented at the 41st Annual Meeting for the American Society for Cell Biology, Washington, D.C., 2001
Abstract
PIR and iProClass for Functional Genomics/Proteomics
Barker, W.C., Castro-Alvear, J., Chen, Y., Hu, Z., Huang, H., Ledley, R.S., Lewis, K.C., Orcutt, B.C., Suzek, B., Vinayaka, C.R., Wu, C.H., Yeh, L.L., and Zhang, J
Presented at the 41st Annual Meeting for the American Society for Cell Biology, Washington, D.C., 2001
Abstract
Comprehensive Superfamily and Function Classification of Protein Sequences
Huang, H., Barker, W.C., Yeh, L.S., and Wu, C.H.
Presented at the Fifth Annual Conference On Computational Genomics, Baltimore, Maryland, 2001
Abstract
PIR and iProClass for Functional Genomics/Proteomics
Barker, W.C., Castro-Alvear, J., Chen, Y., Hu, Z., Huang, H., Ledley, R.S., Lewis, K.C., Orcutt, B.C., Suzek, B., Vinayaka, C.R., Wu, C.H., Yeh, L.L., and Zhang, J
Presented at the Fifth Annual Conference On Computational Genomics, Baltimore, Maryland, 2001
Abstract
PIR Web-Based Tools and Databases for Genomic and Proteomic Research
Barker, W.C., Chen, Y., Hu, Z., Huang, H., Lewis, K., Orcutt, B.C., Yeh, L.L., Wu, C.H.
Presented at the 9th International Conference on Intelligent Systems for Molecular Biology (ISMB), Copenhagen, Denmark, 2001
Abstract
Protein Information Resource: A Community Resource for Expert Annotation of Protein Data
Barker, Winona. C., Chen, Yongxing, Huang, Hongzhan, Ledley, Robert S., Lewis, Kali C., Orcutt, Bruce C., Vinayaka, C.R., Yeh, Lai-Su L., Zhang, Jian, Wu, Cathy H
Presented at the 15th Symposium of the Protein Society, Philadelphia, PA, 2001
Abstract
iProClass: An Integrated Protein Classification Database for Proteomics
Wu, C. H., Chen, Y., Huang, H., Barker, W.C.
Presented at the 15th Symposium of the Protein Society, Philadelphia, PA, 2001
Abstract
Protein Information Resource: A Community Resource for Expert Annotation of Protein Data
Cathy H. Wu and Winona C. Barker
Presented at the Biophysical Society 45th Annual Meeting, Boston, MA, 2001
Abstract
Integrated System for Comprehensive Classification of Protein Sequences
H. Huang, W. C. Barker, L.S. Yeh, and C.H. Wu
Presented at the 13th International Congress for Methods of Protein Structure Analysis (MPSA), 2000.
Abstract
PIR-Class: An Object-Relational Protein Classification Database for Sequence Annotation and Genome Research
Cathy H. Wu, Chunlin Xiao, Zhenglin Hou, and Winona C. Barker
Presented at the ISMB meeting, 2000
Abstract
Object-Relational Protein Sequence Database
Chunlin Xiao, Lai-Su Yeh, Zhenling Hou, Bruce Orcutt, and Cathy Wu
Presented at the 4th Annual Conference on Computational Genomics, Baltimore, MD, 2000
Abstract
iProClass: An Integrated, Comprehensive, and Annotated Protein Classification Database
Cathy H. Wu, Chunlin Xiao, Zhenglin Hou, Hongzhan Huang, and Winona C. Barker
Presented at the 4th Annual Conference on Computational Genomics, Baltimore, MD 2000
Abstract
Protein Active Site Motifs and Structure/Function Relationships
Zhenglin Hou, Chunlin Xiao, Hongzhan Huang, and Cathy H. Wu
Presented at the 4th Annual Conference on Computational Genomics, Baltimore, MD, 2000
Abstract
Cofactor-Binding Homology Domains of the Hybrid Cluster Proteins and the Carbon-monoxide Dehydrogenase Nickel-Containing Chains
Garavelli, J.S., Huang, H., Miller, D.J.
Protein Society Meeting, August 4 - 10, 2000, San Diego, CA
Abstract Poster

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