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HOME / About / Staff Members / Hongzhan Huang
Hongzhan Huang, Ph.D.
Team Lead, Bioinformatics and Research Associate Professor
Protein Information Resource
huang@dbi.udel.edu or hh42@georgetown.edu
Primary Expertise
With background in both mathematics and genetics, Dr. Huang specializes in genomic and proteomic data analysis, bioinformatics database, algorithms and software developments. As the Bioinformatics Team Lead at PIR, he is responsible for the bioinformatics database and software framework development, including iProClass protein centric database integrating more than 120 molecular databases; iProXpress expression analysis system for the functional profiling and pathway/network analysis of large-scale gene expression and proteomic data; PIRSF classification and rule and PIR rule automatic annotation system for the UniProt project; biological network visualization tools and computational genomics framework for next-generation sequence (NGS) data analysis.

Education
B.S.(equiv.), Mathematics, Zhongshan University,Guangzhou, China, 1980
Graduate study, Mathematics, South China Inst. of Technology, Guangzhou, China, 1986
M.S., Genetics,University of California, Davis , CA. 1992
Ph.D., Genetics, University of California, Davis , CA. 1993

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Publications
UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches..
Suzek BE, Wang Y, Huang H, McGarvey PB, Wu CH; the UniProt Consortium.
Bioinformatics. 2014 Nov 13. pii: btu739. [Epub ahead of print]. PubMed PMID: 25398609.
A comprehensive protein-centric ID mapping service for molecular data integration.
Huang H, McGarvey PB, Suzek BE, Mazumder R, Zhang J, Chen Y, Wu CH.
Bioinformatics. Apr 15;27(8):1190-1.. 2011.
Omics-based molecular target and biomarker identification.
Hu ZZ, Huang H, Wu CH, Jung M, Dritschilo A, Riegel AT, Wellstein A.
Methods Mol Biol. 719:547-71. 2011.
Protein-centric data integration for functional analysis of comparative proteomics data.
McGarvey PB, Zhang J, Natale DA, Wu CH, Huang H.
Methods Mol Biol. 694:323-39. 2011.
Structure-guided rule-based annotation of protein functional sites in UniProt Knowledgebase.
Vasudevan S, Vinayaka CR, Natale DA, Huang H, Kahsay RY, Wu CH.
Methods Mol Biol. 694:91-105. 2011.
Protein bioinformatics databases and resources.
Chen C, Huang H, Wu CH.
Methods Mol Biol. 694:3-24. 2011.
Ongoing and future developments at the Universal Protein Resource.
UniProt Consortium.
Nucleic Acids Res. 39(Database issue):D214-9. 2011.
The Protein Ontology: a structured representation of protein forms and complexes.
Natale DA, Arighi CN, Barker WC, Blake JA, Bult CJ, Caudy M, Drabkin HJ, D'Eustachio P, Evsikov AV, Huang H, Nchoutmboube J, Roberts NV, Smith B, Zhang J, Wu CH.
Nucleic Acids Res. 39(Database issue):D539-45. 2011.
Phylogenomic analysis of marine Roseobacters.
Tang K, Huang H, Jiao N, Wu CH.
PLoS One. 5(7):e11604. 2010.
Molecular mechanisms mediating the effect of mono-(2-ethylhexyl) phthalate on hormone-stimulated steroidogenesis in MA-10 mouse tumor Leydig cells.
Fan J, Traore K, Li W, Amri H, Huang H, Wu C, Chen H, Zirkin B, Papadopoulos V.
Endocrinology. 151(7):3348-62. 2010.
From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase.
Hinz U; UniProt Consortium.
Cell Mol Life Sci. 67(7):1049-64. 2010.
Protein Bioinformatics Infrastructure for the Integration and Analysis of Multiple High-Throughput omics Data.
Chen C, McGarvey PB, Huang H, Wu CH.
Adv Bioinformatics. 2010; 2010:423589. 2010.
The Universal Protein Resource (UniProt) in 2010.
UniProt Consortium.
Nucleic Acids Res. 38(Database issue):D142-8. 2010.
Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets.
McGarvey PB, Huang H, Mazumder R, Zhang J, Chen Y, Zhang C, Cammer S, Will R, Odle M, Sobral B, Moore M, Wu CH.
PLoS One. 4(9):e7162. 2009.
The Universal Protein Resource (UniProt) 2009.
UniProt Consortium.
Nucleic Acids Res. 37(Database issue):D169-74. 2009.
Integrated Bioinformatics for Radiation-Induced Pathway Analysis from Proteomics and Microarray Data.
Hu ZZ, Huang H, Cheema A, Jung M, Dritschilo A, Wu CH.
J Proteomics Bioinform. 1(2):47-60. 2008.
Protein Bioinformatics.
McGarvey P, Huang H, Wu CH.
in: Medical Applications of Mass Spectrometry. Part III Biomolecules, Chapter 10:203-222. K Vekey, A Telekes, A Vertes (Eds.) Elsevier Science. 2008.
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(Database issue):D884-91. 2008.
Integration of bioinformatics resources for functional analysis of gene expression and proteomic data.
Huang H, Hu ZZ, Arighi CN, Wu CH.
Front Biosci. 12:5071-88. 2007.
UniRef: comprehensive and non-redundant UniProt reference clusters.
Suzek BE, Huang H, McGarvey P, Mazumder R, Wu CH.
Bioinformatics. 23(10):1282-8. 2007.
Challenges and solutions in proteomics.
Huang H, Shukla HD, Cathy W, Satya S.
Curr Genomics. 8(1):21-8. 2007.
PIRSF family classification system for protein functional and evolutionary analysis.
Nikolskaya AN, Arighi CN, Huang H, Barker WC, Wu CH.
Evol Bioinform Online. 2:197-209. 2007.
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 C.
Int J Mass Spectrom. 259(1-3):147-160. 2007.
The Universal Protein Resource (UniProt).
UniProt Consortium.
Nucleic Acids Res. 35(Database issue):D193-7. 2007.
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(11):3135-44. 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 Res. 34(Database issue):D187-91. 2006.
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 Res. 33(Database issue):D154-9. 2005.
Family classification and integrative associative analysis for protein functional annotation.
Huang H, Nikolskaya AN, Vinayaka CR, Chung S, Zhang J, Wu CH.
in: Trends in Bioinformatics Research. Chapter II:33-57. PV Yan (Ed.), Nova Science Publishers, Inc. 2005.
Gene and protein profiling of the response of MA-10 Leydig tumor cells to human chorionic gonadotropin.
Li W, Amri H, Huang H, Wu C, Papadopoulos V.
J Androl. 25(6):900-13. 2004.
The iProClass integrated database for protein functional analysis.
Wu CH, Huang H, Nikolskaya A, Hu Z, Barker WC.
Comput Biol Chem. 28(1):87-96. 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 Res. 32(Database issue):D115-9. 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 Res. 32(Database issue):D112-4. 2004.
Protein family classification and functional annotation.
Wu CH, Huang H, Yeh LS, Barker WC.
Comput Biol Chem. 27(1):37-47. 2003.
iProClass: an integrated database of protein family, function and structure information.
Huang H, Barker WC, Chen Y, Wu CH.
Nucleic Acids Res. 31(1):390-2. 2003.
The Protein Information Resource.
Wu CH, Yeh LS, Huang H, Arminski L, Castro-Alvear J, Chen Y, Hu Z, Kourtesis P, Ledley RS, Suzek BE, Vinayaka CR, Zhang J, Barker WC.
Nucleic Acids Res. 31(1):345-7. 2003.
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 HW, Orcutt BC, Suzek BE, Tsugita A, Vinayaka CR, Yeh LS, Zhang J, Barker WC.
Nucleic Acids Res. 30(1):35-7. 2002.
iProClass: an integrated, comprehensive and annotated protein classification database.
Wu CH, Xiao C, Hou Z, Huang H, Barker WC.
Nucleic Acids Res. 29(1):52-4. 2001.
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 HW, Orcutt BC, Pfeiffer F, Tsugita A, Vinayaka CR, Xiao C, Yeh LS, Wu C.
Nucleic Acids Res. 29(1):29-32. 2001.
PIR: a new resource for bioinformatics.
McGarvey PB, Huang H, Barker WC, Orcutt BC, Garavelli JS, Srinivasarao GY, Yeh LS, Xiao C, Wu CH.
Bioinformatics. 16(3):290-1. 2000.
ProClass protein family database.
Huang H, Xiao C, Wu CH.
Nucleic Acids Res. 28(1):273-6. 2000.
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 HW, Tsugita A, Wu C.
Nucleic Acids Res. 28(1):41-4. 2000.
ProClass Protein Family Database.
Wu C, Shivakumar S and Huang H.
Nuc. Acids. Res. 27: 272-274 1999.
Quantitative analysis of correlations among flower traits in gerbera.
Huang H and Harding J.
Theor. Appl. Genet. 97: 312-322. 1998.
Gene family identification using neural networks.
Wu C and Huang H.
Proceedings of the World Multiconference on Systemics, Cybernetics and Informatics (SCI'98). 267-273. 1998.
Estimation of genetic variance components and heritabilities for cut-flower yield in gerbera using least squares and maximum likelihood methods.
Harding J, Huang H and Byrne T.
Euphytica. 88: 55-60. 1996.
The effects of inbreeding on cut-flower yield in gerbera.
Huang H, Harding J, Byrne T and Famula T.
Euphytica. 1995.
Estimation of long-term genetic improvement for gerbera cut-flower yield using the best linear unbiased prediction (BLUP) procedure.
Huang H, Harding J, Byrne T and Famula T.
Theor. Appl. Genet. 91:790-794. 1995.
Long-term genetic improvement of cut-flower yield in gerbera.
Huang H, Harding J and Byrne T.
Hort. Science. 29(5): 435. 1994.
Effects of inbreeding on flower yield in gerbera.
Huang H, Harding J and Byrne T.
Hort Science. 27(6): 586. 1992.
Maternal, paternal, additive, and dominance components of variance in gerbera.
Harding J, Huang H and Byrne T.
Theor. Appl. Genet. 82: 756-760. 1991.
Multi-trait selection in flower crops.
Harding J, Byrne T, Huang H and Yu Y.
In: Harding J et al (eds.) Genetic and breeding of Ornamental species, Kluwer Academic Publisher, Dordrecht. 1991.
Quantitative analysis of correlations among flower traits in gerbera hybrida compositae, 2. Direct and Mean correlated response to selection.
Huang H, Harding J, Byrne T and Huang N.
Theor. Appl. Genet. 80: 559-563. 1990.
Quantitative analysis of correlations among flower traits in gerbera hybrida compositae, 1. genetic and environmental correlation.
Harding J, Huang H, Byrne T and Huang N.
Theor. Appl. Genet. 80: 552-558. 1990.


Revised 04/05/2011

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