Areas of Support

Bioinformatics and computational biology support include the development of customized tools and approaches to support faculty led research and advanced data analysis and mining for research projects and funding application, those include:

• cDNA microarray, Affymetrix GeneChip, ChIP-chip, and microRNA data analyses.
• Genome scale sequence analysis: ESTs, genomes, etc.
• Functional promoter and genetic network analyses.
• Biological data analysis and mining using statistical approaches.
• Pathway analyses, Protein and metabolic profiling.
• Development of bioinformatics tools for the above analyses.

Current Collaborative Research Projects

• "Integration of Clinical, Genomic, and Proteomic Data Using a Bioinformatic Approach" with Drs. Stanley Schwartz and Chiu-bin Hsian from the Dept. of Medicine.
• "Genome-wide Study of Iron Homeostasis" with Dr. James F. Collins from the Dept. of Exercise and Nutrition Sciences.
• "Studies of Maternal and Neonatal Immunity" with Dr. Thomas Tomasi from RPCI.
• "The Role of Protein Arginine Methlation in Gene Expression" with Dr. Michael Yu from the Biological Science Dept.
• "Innate Immunity in Oral Candidiasis" with Dr. Sarah L. Gaffen from the Dept. of Oral Biology.
• "Salivary Transcriptome diagnostics for Sjogren's Syndrom Detection" with Dr. Lida Radfar from the Dept. of Oral Biology.
• "Investigation of a New Murine Model for Sjogren's Syndrome" with Dr. Julian L. Ambrus from the School of Medicine and Biological Sciences.
• "Enabling High Throughput Analysis of Clinical Samples" with Dr. Wilfredo Mojica from the Dept. of Pathology and Anatomical Sciences.
• "Development of a Vaccine for Moraxella Catarrhalis" with Tim Murphy from the Dept. of Medicine.
• "Cellular Metabolism of Vanadium and its effect on Diabetes" with Dr. Gail Willsky from the Dept. of Biochemistry.

Research and Research Interests

My main research lies in data mining and developing new methodology for the analysis of experimental data from areas in the biomedical sciences including RNA profiling, genomics, systems biology, and proteomics. Much of the work occurs through collaborative projects with other faculty members in the university. I also develop computational and statistical methodology and approaches for expression analysis, comparative analysis of genomic DNA sequence, and the study of genetic networks. More specifically, I currently have the following research foci:

Genetic networks: Conducting genome-wide studies of regulatory elements to elucidate the regulatory logic of transcription factors and their corresponding binding sites in controlling gene expression. Applying the developed statistical and computational approaches from the above research to collaborative projects.

Data mining and analysis:Analyzing patterns of gene expression and interrelating them with data related to other information about these genes. Developing statistical and computational approaches, which are robust yet simple to apply, for both Affymetrix GeneChip and cDNA microarray data processing and analysis.

Large-scale sequence analysis: Comparative analysis of microbial genomic DNA sequences to elucidate the evolutionary dynamics of virulence genes, their relationship, and lateral gene transfer between species and strains.

Recent Publications

1. Lindemann MJ, Zihua Hu, M Benczik, KD Liu, SL Gaffen (2008) Differential Regulation of the IL-17 Receptor by yc Cytokines: Inhibitory Signaling by the PI 3-kinase Pathway J Biol Chem.
2. Ananthi J. Asirvatham, Christopher J. Gregorie, Zihua Hu, William J. Magner and Thomas B. Tomasi (2008) MicroRNA Targets in Immune Genes and the Dicer/Argonaute and ARE Machinery Components. Molecular Immunology.
3. Ruckdeschel E, C Kirkham, AJ Lesse, Zihua Hu; TF Murphy (2008) Mining the Moraxella catarrhalis Genome: Identification of Potential Vaccine Antigens Expressed during Human Infection. Infect Immun .
4. James F. Collins, Zihua Hu, Laura M. Garrick, Michael D. Garrick, Richard W. Browne (2008)Induction of Arachidonate 12-Lipoxygenase in Intestine of Fe-Deficient Rats Results in Production of Biologically Active Lipid Mediators. Am J Physiol Gastrointest Liver Physiol.
5. Zihua Hu*, Boyu Hu, and Jamie F. Collins (2007) Prediction of Synergistic Transcription Factors by Function Conservation. Genome Biology, 8:R257.
6. Jamie F. Collins* and Zihua Hu* (2007) Promoter Analysis of Rat Duodenal Genes Induced During Iron-Deficiency Reveals Enrichment of Conserved SP1 Binding Sites. BMC Genomics, 8:420.
7. Bindukumar B, SD Mahajan, JL Reynolds, Zihua Hu, DE Sykes, R Aalinkeel, and SA Schwartz (2007) Genomic and Proteomic Analysis of The Effects of Cannabinoids on Normal Human Astrocytes (in printing).
8. Ravikumar Aalinkeel, Zihua Hu, Bindukumar Balakrishnan, Donald E Sykes, Jessica L. Reynolds, Supriya D. Mahajan and Stanley A Schwartz. Genomic Analysis Highlights the Role of the JAK-STAT Signaling in the Anti Proliferative Effects of Dietary Flavonoid- "Ashwagandha" in Prostate Cancer Cells (submitted).
9. Zihua Hu*, GR Wilsky (2006) Utilization of Two Sample t-test Statistics from Redundant Probe Sets to Evaluate Different Probe Set Algorithms in GeneChip Studies. BMC Bioinformatics, 7:12.
10. Shen F, Zihua Hu, J Goswami and SL Gaffen (2006) Identification of Common Transcriptional Regulatory Elements in Interleukin-17 Target Genes. J Biol Chem. 281:24138-24148.
11. Mahajan SD, Zihua Hu, JL Reynolds, R Aalinkeel, SA Schwartz and MPN Nair (2006) Methamphetamine Modulates Gene Expression Patterns in Monocyte Derived Mature Dendritic Cells: Implications for HIV-1 Pathogenesis. Mol Diagn Ther. 10:257-269.
12. Willsky GR, L-H Chi, Y Liang, DP Gaile, Zihua Hu, DC Crans (2006) Diabetes Altered Gene Expression in Rat Skeletal Muscle Corrected by Oral Administration of Vanadyl Sulfate. Physiological Genomics,26:192-201.
13. Gallo SM, L Li, Zihua Hu and MS Halfon (2005) REDfly: A Regulatory Element Database for Drosophila. Bioinformatics, 22:381-383.
14. Guo M, M Rupe , O Danilevskay , X Yang and Zihua Hu (2003) Genome-wide mRNA Profiling Reveals Heterochronic Allelic Variation and a New Imprinted Gene in Hybrid Maize Endosperm, Plant J, 36:30-44.

Book Chapters and Presentations

1.  Zihua Hu (2004) "DNA Microarray and Data Analysis". In "Introduction to Bioinformatics", ZhengzhouUniversityPress, pp 153-174.
2. Zihua Hu (2004) "Molecular Databases and Their Applications". In "Introduction to Bioinformatics", ZhengzhouUniversity Press, pp 75-110.
3. Zihua Hu and Ping Liang (2004) "DNA and Protein Sequences Analysis". In "Introduction to Bioinformatics", ZhengzhouUniversityPress, pp 111-135.
4. Zihua Hu and Wei Li (2004) "Elements of Statistics". In "Introduction to Bioinformatics", ZhengzhouUniversity Press, pp 221-261.
5. Browne RW, Garrick MD, Garrick LM, Zihua Hu. Altered Arachidonic Acid Metabolism in the Intestine of Iron and Iron/Copper-Deficient Rats: Strong Induction of Arachidonate 12-Lipoxygenase. Podium Presentation. 2^nd Congress of the International BioIron Society, Kyoto Japan, April 2007. 
6. Collins JF, Zihua Hu. Microarray Analysis of Rat Duodenum during Iron- and Copper Deficiency. Poster presented at Experimental Biology, WashingtonD.C. April 2007. 
7. Browne RW, Zihua Hu. Arachidonate 12-Lipoxygenase Is Strongly Induced by Iron-Deficiency and Is Expressed in Rat Small Intestine and Colon. Poster presented at Digestive Disease Week Meeting, WashingtonD.C.May 2007. 
8. Collins JF and Zihua Hu(2006) Identification of Putative Transcriptional Regulatory Pathways Mediating the Genomic Response to Iron-deficiency in Rat Duodenum. Gastroenterology130:A540. 
9. Collins JF, Zihua Hu, S Rakka, E Kilcourse and KV Kowdley (2006) Novel Differentially Expressed Genes Revealed by Microarray Analysis of Duodenum in Patients with Disorders of Iron Homeostasis. Oral abstract presentation. Digestive Disease Week Annual Meeting, Los Angeles,CA. 
10. Zihua Hu, Collins JF. Copper Deprivation Results in Alterations in Intestinal Gene Expression Distinct From Those Caused By Iron-Deficiency. Poster presented at the 6^th International Copper Meeting. Alghero, Sardinia,Italy, October, 2006.
11. Ravia JJ, RM Stephen, Zihua Hu, LM Garrick, MD Garrick and JF Collins (2005) Microarray Analyses Reveal Unique Gene Expression Patterns in The Intestinal Mucosa of DMT1-deficient, Belgrade Rats. Book of Abstracts, International BioIron Society, 94: p223

Teaching

Spring 2008           Instructorfor "Introduction of Bioinformatics and Computational Biology"BCH519 for graduate studentsSpring 2007           Instructor for "Introduction of Bioinformatics and Computational Biology"BCH519 for graduate students

Recent External Research Support

01/01/2005 - 12/31/2009
NIH (AI 28304; $1,250,000)
"Development of a Vaccine for Moraxella Catarrhalis"
Role: Co-PI

© Zihua Hu, 2007