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	Refereed Papers	(Some files are in PDF format)
	Books/Book Chapters
	Documents/Bulletins

Refereed Papers
An emerging cyberinfrastructure for biodefense pathogen and pathogen host data. Zhang C, Crasta O, Cammer S, Will R, Kenyon R, Sullivan D, Yu Q, Sun W, Jha R, Liu D, Xue T, Zhang Y, Moore M, McGarvey P, Huang H, Chen Y, Zhang J, Mazumder R, Wu C, Sobral B. Nucleic Acids Res., 36:D884-D891, 2008.
Computational analysis and identification of amino acid sites in dengue E proteins relevant to development of diagnostics and vaccines. Mazumder R, Hu ZZ, Vinayaka CR, Sagripanti JL, Frost SD, Kosakovsky Pond SL and Wu CH. Virus Genes 35(2):175-186, 2007.
Integration of bioinformatics resources for functional analysis of gene expression and proteomic data. Huang H, Hu ZZ, Arighi CN, Wu CH. Front Biosci. 12, 5071-5088, 2007.
UniRef: comprehensive and non-redundant UniProt reference clusters. Suzek BE, Huang H, McGarvey P, Mazumder R, Wu CH. Bioinformatics 23(10):1282-1288, 2007.
Challenges and solutions in proteomics. Huang H, Shukla H, Saxena S, and Wu, C.H. Current Genomics 8 (in press)
New developments in the InterPro database. Mulder NJ, Apweiler R, Attwood TK, Bairoch A, et al, Wu CH, Yates C. Nucleic Acids Res. 35(Database issue):D224-8, 2007.
The Universal Protein Resource (UniProt). UniProt Consortium. Nucleic Acids Res. 35(Database issue):D193-7, 2007.
A comparison study on algorithms of detecting long forms for short forms in biomedical text Torii M, Liu HF, Hu ZZ and Wu, C.H. Proceedings of ACM First International Workshop on Text Mining in Bioinformatics, TMBIO 2006. BMC Bioinformatics 8(Suppl 9):S5, 2007.
Framework for a Protein Ontology Natale DA, Arighi CN, Barker W, Blake J, Chang T, Hu ZZ, Liu H, Smith B, Wu CH. Proceedings of ACM First International Workshop on Text Mining in Bioinformatics, TMBIO 2006. BMC Bioinformatics 8(Suppl 9):S1, 2007.
Dependence network modeling for biomarker identification. Qiu P, Wang J, Ray Liu KJ, Hu ZZ, Wu CH. Bioinformatics 23:198-206, 2006.
Comparative bioinformatics analyses and profiling of lysosome-related organelle proteomes. Hu ZZ, Valencia JC, Huang H, Chi A, Shabanowitz J, Hearing VJ, Appella E, Wu CH. Int J Mass Spec 259:147-160, 2006.
Proteomic and Bioinformatic Characterization of the Biogenesis and Function of Melanosomes. Chi A, Valencia JC, Hu ZZ, Watabe H, Yamaguchi H, Mangini NJ, Huang H, Canfield VA, Cheng KC, Yang F, Abe R, Yamagishi S, Shabanowitz J, Hearing VJ, Wu C, Appella E, Hunt DF. J Proteome Res 5:3135-3144, 2006.
Quantitative Assessment of Dictionary-based Protein Named Entity Tagging. Liu H, Hu ZZ, Torii M, Wu C, Friedman C. J Am Med Inform Assoc 13:497-507, 2006.
Substring selection for biomedical document classification. Han B, Obradovic Z, Hu ZZ, Wu CH, Vucetic S. Bioinformatics 22:2136-42, 2006.
Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties. Petrova NV, Wu CH. BMC Bioinformatics. 2006 7:312.
An online literature mining tool for protein phosphorylation. Yuan X, Hu ZZ, Wu HT, Torii M, Narayanaswamy M, Ravikumar KE, Vijay-Shanker K, Wu CH. Bioinformatics. 2006 22(13):1668-1669.
PIRSF Family Classification System for Protein Functional and Evolutionary Analysis. Nikolskaya AN, Arighi CN, Huang H, Barker WC, Wu CH. Evolutionary Bioinformatics Online 2:209-221, 2006.
BioThesaurus: a web-based thesaurus of protein and gene names Liu HF, Hu ZZ, Zhang J, Wu CH. Bioinformatics 22:103-105, 2006.
The Universal Protein Resource (UniProt): an expanding universe of protein information. Wu CH, Apweiler R, Bairoch A, Natale DA, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Mazumder R, O'donovan C, Redaschi N, Suzek B. Nucleic Acids Research 34: D187-91, 2006.
DynGO: a tool for visualizing and mining of Gene Ontology and its associations. Liu H, Hu ZZ, Wu CH. BMC Bioinformatics 6: 201, 2005.
Computational identification of strain-, species- and genus-specific proteins Mazumder R, Natale D, Murthy S, Thiagarajan R, Wu CH. BMC Bioinformatics 6: 279, 2005.
Plant Protein Annotation in the UniProt Knowledgebase Schneider M, Bairoch A, Wu CH, Apweiler R. Plant Physiology 138: 59-66, 2005.
Literature mining and database annotation of protein phosphorylation using a rule-based system Hu ZZ, Narayanaswamy M, Ravikumar KE, Vijay-Shanker K, Wu CH. Bioinformatics 21(11): 2759-2765, 2005.
Protein name tagging guidelines: lessons learned Mani I, Hu Z, Jang SB, Samuel K, Krause M, Phillips J, Wu CH. Comparative and Functional Genomics, 6(1-2): 72-76, 2005.
The Universal Protein Resource (UniProt) Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LS. Nucleic Acids Research, 33: D154-159, 2005.
InterPro, progress and status in 2005 Mulder NJ, Apweiler, R.,Attwood TK, Bairoch A, et al. and Wu CH. Nucleic Acids Research, 33: D201-205, 2005.
iProLINK: An Integrated Protein Resource for Literature Mining Hu ZZ, Mani I, Hermoso V, Liu H and Wu CH . Computational Biology and Chemistry, 28: 409-416, 2004.
Update on human genome completion and annotations: Protein Information Resource Wu CH & Nebert DW. Human Genomics, 1: 229-233, 2004.
A study of text categorization for model organism databases Liu H & Wu CH. Proceedings of BioLINK 2004: Linking Biological Literature, Ontologies and Databases, pp. 25-32, 2004.
BioTagger: a biological entity tagging system Liu H, Wu CH and Friedman C. Proceedings of BioCreative Workshop - A critical assessment of text mining methods in molecular biology, Granada, Spain, March 28-31, 2004.
The iProClass Integrated database for protein functional analysis Wu CH, Huang H, Nikolskaya A, Hu Z, Yeh LS, Barker WC. Computational Biology and Chemistry, 28: 87-96, 2004.
Protein sequence databases Apweiler R, Bairoch A, Wu CH. Current Opinion in Chemical Biology, 8: 76-80, 2004.
PIRSF: family classification system at the Protein Information Resource Wu CH, Nikolskaya A, Huang H, Yeh LS, Natale DA, Vinayaka CR, Hu ZZ, Mazumder R, Kumar S, Kourtesis P, Ledley RS, Suzek BE, Arminski L, Chen Y, Zhang J, Cardenas JL, Chung S, Castro-Alvear J, Dinkov G, Barker WC. Nucleic Acids Research, 32: D112-D114, 2004.
UniProt: the Universal Protein knowledgebase Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LS. Nucleic Acids Research, 32: D115-D119, 2004.
The PIR integrated protein databases and data retrieval system Huang H, Hu ZZ, Suzek BE and Wu CH. Data Science 3: 163-174, 2004.
Gene and protein profiling of the acute response of MA-10 Leydig tumor cells to human chorionic gonadotropin. Li W, Amri H, Huang H, Wu CH and Papadopoulos V. Journal of Andrology, 25: 900-913, 2004.
BIO-AJAX: An extensible framework for biological data cleaning. Herbert KG, Gehan NH, Piel WH, Wang JTL and Wu CH. SIGMOD Record, 33: 51-57, 2004.
Protein family classification and functional annotation Wu CH, Huang H, Yeh LS, Barker WC. Computational Biology and Chemistry, 27: 37-47, 2003.
iProclass: an integrated database of protein family classification, function and structure information Huang H, Barker WC, Chen Y, Wu CH. Nucleic Acids Research, 31: 390-392, 2003.
The Protein Information Resource Wu CH, Yeh LS, Huang H, Arminski L, Castro-Alvear J, Chen Y, Hu ZZ, Ledley RS, Kourtesis P, Suzek BE, Vinayaka CR, Zhang J, Barker WC. Nucleic Acids Research, 31: 345-347, 2003.
Accomplishments and challenges in literature data mining for biology Hirschman L, Park JC, Tsujii J, Wong L, Wu CH. Bioinformatics 18:1553-1561, 2002.
The Protein Information Resource: an integrated public resource of functional annotation of proteins Wu CH, Huang H, Arminski L, Castro-Alvear J, Chen Y, Hu ZZ, Ledley RS, Lewis KC, Mewes H, Orcutt BC, Suzek BE, Tsugita A, Vinayaka CR, Yeh LS, Zhang J, Barker WC. Nucleic Acids Research, 30: 35-37, 2002.
Protein Information Resource: a community resource for expert annotation of protein data Barker WC, Garavelli JS, Hou Z, Huang H. Ledley RS, McGarvey PB, Mewes H, Orcutt BC, Pfeiffer F, Tsugita A, Vinayaka CR, Xiao C, Yeh LS, Wu CH. Nucleic Acids Research, 29: 29-32, 2001.
iProclass: an integrated, comprehensive and annotated protein classification database. Wu CH, Xiao C, Hou Z, Huang H, Barker WC. Nucleic Acids Research, 29: 52-54, 2001.
The RESID Database of protein structure modifications and the NRL-3D Sequence-Structure Database Garavelli JS, Hou Z, Pattabiraman N, Stephens RM. Nucleic Acids Research, 29: 199-201, 2001.
The Protein Information Resource (PIR) Barker WC, Garavelli JS, Huang H, McGarvey PB, Orcutt BC, Srinivasarao GY, Xiao C, Yeh LS, Ledley RS, Janda JF, Pfeiffer F, Mewes H, Tsugita A, Wu CH. Nucleic Acids Research, 28: 41-44, 2000.
ProClass protein family database Huang H, Xiao C, Wu CH. Nucleic Acids Research, 28: 273-276, 2000.
The RESID Database of protein structure modifications: 2000 update Garavelli JS. Nucleic Acids Research, 28: 209-211, 2000.
PIR: A New Resource for Bioinformatics McGarvey PB, Huang H, Barker WC, Orcutt BC, Garavelli JS, Srinivasarao GY, Yeh LL, Xiao C, Wu CH. Bioinformatics. 16, 290-291, 2000.
The PIR-International Protein Sequence Database Barker WC, Garavelli JS, McGarvey PB, Marzec CR, Orcutt BC, Srinivasarao GY, Yeh LL, Ledley RS, Mewes H, Pfeiffer F, Tsugita A, Wu CH. Nucleic Acids Research, 27, 39-43, 1999.
Database of Protein Sequence Alignments: PIR-ALN Srinivasarao GY, Yeh LL, Marzec CR, Orcutt BC, Barker WC. Nucleic Acids Research, 27: 284-285, 1999.
The RESID Database of Protein Structure Modifications Garavelli JS. Nucleic Acids Research, 27: 198-199, 1999.
PIR-ALN: A Database of Protein Sequence Alignments Srinivasarao GY, Yeh LL, Marzec CR, Orcutt BC. Bioinformatics 15: 382-390, 1999.
The PIR-International Protein Sequence Database Barker WC, Garavelli JS, Haft DH, Hunt LT, Marzec CR, Orcutt BC, Srinivasarao GY, Yeh LL, Ledley RS, Mewes H, Pfeiffer G, Tsugita A. Nucleic Acids Research, 26: 27-32, 1998.

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Books/Book Chapters
Bioinformatic databases. Herbert KG, Spirollari J, Wang JTL, Piel WH, Westbrook J, Barker WC, Hu ZZ and Wu, C.H. Encyclopedia of Computer Science and Engineering (Cassie Craig Assistant Editor), John Wiley & Sons, Ltd, 2007.
Identification of sensory and signal-transducing domains in two-component signaling systems Michael Y. Galperin and Anastasia N. Nikolskaya Volume 422 of Methods in Enzymology 422:47-74, 2007.
The PIR superfamily (PIRSF) classification system Barker WC, Mazumder R, Nikolskaya A. and Wu CH. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, Part 3. Proteomics, Volume 6, Section 6. Proteome Families, Dunn, M. J. (Ed.) John Wiley & Sons, Ltd, 2005.
Protein Bioinformatics McGarvey P, Huang H. and Wu CH. Medical Applications of Mass Spectrometry. Vekey, K., Telekes, A., Vertes, A. (Eds.) Elsevier Science pp197-216, 2007.
Family classification and integrative associative analysis for protein functional annotation Huang, H., Nikolskaya AN, Vinayaka CR, Chung S, Zhang J and Wu CH Trends in Bioinformatics Research. Peter V. Yan (Ed.), Nova Science Publishers, Inc. pp. 33-57, 2005.
Information flow and data integration of databanks Wu CH and Barker WC. Database Annotation in Molecular Biology. AM Lesk (Ed.), John Wiley & Sons, Ltd. pp.187-201, 2005.
Annotation of protein sequences. Barker WC and Wu CH. Database Annotation in Molecular Biology, AM Lesk (Ed.), John Wiley & Sons, Ltd. pp.131-147, 2005.
A family classification approach to functional annotation of proteins Wu CH and Barker WC, The Practical Bioinformatician. L. Wong (Ed.), World Scientific, NJ, pp. 417-434, 2004.
Large-scale, classification-driven, rule-based functional annotation of proteins. Natale DA, Vinayaka CR and Wu CH. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. Bioinformatics Volume, Subramaniam, S. (Ed.) John Wiley & Sons, Ltd, 2004.
Computational Biology and Genome Informatics Wang JTL, Wu CH, Wang PP. World Scientific, 2003.
Neural Networks and Genome Informatics Wu CH & McLarty JW. Elsevier Science, 2000.
Atlas of Protein Sequence and Structure Dayhoff, M. Vol 1-5, suppl. 1-3. National Biomedical Research Foundation, 1965-1978.

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Documents/Bulletins
PIRSF A Proposal for the PIRSF Classification System (2003) PIR Guidelines for Assigning Names to PIRSFs (2004)
Protein name tagging guidelines PIR Guidelines for Protein Name Tagging Version 1.0 (2003) PIR Guidelines for Protein Name Tagging Version 2.0 (2004)
Guide for Feature AnnotationsFeatures Document
Database Definition Document PIR-International Protein Sequence Database (PSD) Database Definition Document: The Protein Sequence Component (1994)
ATLAS User's Guide Guide to the Atlas of Protein and Genomic Sequences on CD-ROM (1996)

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Last Updated 01/14/2008