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Center for Computational Research

Zihua Hu, PhD

Portrait

Bioinformatics Computational Scientist

Dr. Hu has been with the Center for Computational Research since 2002.  He works with users interested in bioinformatics resources and provides support and assistance to UB faculty and Roswell Park researchers.

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:

  • Gene regulation: including functional promoter, transcriptional regulatory network, and miRNA analyses.
  • RNA-Seq, Chip-seq, Chip-RNA, ChiP-chip, Affymetrix GeneChip, and cDNA microRNA data analyses.
  • Genome scale sequence analysis: ESTs, genomes, etc.
  • Biological data analysis and mining using statistical approaches.
  • Pathway analyses, Protein and metabolic profiling.
  • Development of bioinformatics tools for the above analyses.

Research and Research Interests:

I am currently pursuing a variety of computational and genomics topics and collaborating with colleagues on large-scale genomics projects, including developing statistical and computational approaches for gene expression, transcriptional regulatory network, and large-scale sequence analyses. My independent research interest is on the global gene regulation at both transcriptional and post-transcriptional levels. The major focus is to use computational approaches to integrate high-throughput biological data to ask questions and understand gene regulation mechanisms in a systems level. These include:

Transcriptional Regulation of Gene expression. Regulation of gene expression plays a key role in many cellular processes, including proliferation, senescence and development. Transcription is a major target for regulation of gene expression in all organisms, and failure to correctly regulate transcription is a cause of many diseases, notably cancer. Indeed, many human oncogenes are themselves transcriptional regulators. Transcriptional regulation also plays a key role in the virulence of many human pathogens. Therefore it is vital to understand the mechanisms by which transcription is regulated. My research is focused on the mechanisms of transcriptional regulation of disease-related gene expression;My research also includes conducting genome-wide studies of regulatory elements to elucidate the regulatory logic of transcription factors and their corresponding binding sites in controlling gene expression and applying the developed statistical and computational approaches from the above research to collaborative projects.

Post-transcriptional Gene Regulation by microRNAs. microRNAs will shape biology and change the traditional concepts of the molecular biology. My research focus is to uncover the widespread influence of miRNAs on disease-related gene expression.

Genetic Variation and Diseases.  Genetic variations play important roles in the regulation of gene expression such as miRNA and SNPs.  We are interested in addressing the questions as how different miRNAs and SNPs might contribute separately or synergistically to specific phenotypes such as diseases.

Recent Publications:

  1. Bruno AE, Li L, Kalabus JL, Pan Y, Yu A, Hu Z* (2012) “miRdSNP: a database of disease-associated SNPs and microRNA target sites on 3'UTRs of human genes”. BMC Genomics. 13:44.
  2. Hu BH, Cai Q, Hu Z, Patel M, Bard J, Jamison J, Coling D (2012) “Metalloproteinases and their associated genes contribute to the functional integrity and noise-induced damage in the cochlear sensory epithelium”. J Neurosci.32:14927-41.
  3. Shu W, Lin Y, Hua R, Luo Y, He N, Fang L, Tan J, Lu J, Hu Z, Yuan Z (2012) “Cutaneomucosal venous malformations are linked to the TIE2 mutation in a large Chinese family”. Exp Dermatol. 21:456-7.
  4. Kuo SM, Burl LR, Hu Z (2012) “Cellular phenotype-dependent and -independent effects of vitamin C on the renewal and gene expression of mouse embryonic fibroblasts”. PLoS One. 7(3):e32957.
  5. Hu Z*, Bruno AE (2011) “The Influence of 3'UTRs on MicroRNA Function Inferred from Human SNP Data”.  Comp Funct Genomics. 910769.
  6. Willsky GR, Chi LH, Godzala M, Kostyniak PJ, Smee JJ, Trujillo AM, Alfano JA, Ding W, Hu Z, Crans DC (2011) “Anti-diabetic effects of a series of vanadium dipicolinate complexes in rats with streptozotocin-induced diabetes”. Coord Chem Rev. 255(19-20):2258-2269.
  7. Zihua Hu *  , Gulec S, Collins JF (2010) "Cross-Species Comparison of Genome-Wide Gene Expression Profiles Reveals a Preferential Induction of Hypoxia Inducible Factor Responsive Genes in Iron Deprived Intestinal Epithelial Cells." Am J Physiol Cell Physiol .
  8. Zihua Hu * , S Gallo (2010) "Identification of interacting transcription factors controlling gene expression in human tissues." BMC Genomics;11:49 .
  9. Zihua Hu *  (2009) "Insight into microRNA regulation by analyzing the characteristics of their targets in humans." BMC Genomics;10:594 .
  10. Mahajan SD, Aalinkeel R, Reynolds JL, Nair BB, Sykes DE, Zihua Hu  , Bonoiu A, Ding H, Prasad PN, Schwartz SA (2009) "Therapeutic targeting of "DARPP-32": a key signaling molecule in the dopiminergic pathway for the treatment of opiate addiction." Int Rev Neurobiol. 88:199-222 .
  11. 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 ;283(20):14100-14108.
  12. 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; 45(7):1995-2006 .
  13. 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; 76(4):1599-1607 .
  14. 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 ;294(4):G948-962.
  15. Ravikumar Aalinkeel, Zihua Hu , Binduku1-11.ar Balakrishnan, Donald E Sykes, Jessica L. Reynolds, Supriya D. Mahajan and Stanley A Schwartz (2008) "Genomic Analysis Highlights the Role of the JAK-STAT Signaling in the Anti Proliferative Effects of Dietary Flavonoid- "Ashwagandha" in Prostate Cancer Cells." eCAM, doi:10.1093/ecam/nem184 .
  16. Bindukumar B, SD Mahajan, JL Reynolds, Zihua Hu  , DE Sykes, R Aalinkeel, and SA Schwartz (2008) "Genomic and Proteomic Analysis of The Effects of Cannabinoids on Normal Human Astrocytes." Brain Research, 119:1-11 .
  17. Zihua Hu * , Boyu Hu, and Jamie F. Collins (2007) "Prediction of Synergistic Transcription Factors by Function Conservation." Genome Biology, 8:R257 .
  18. Zihua Hu *  , Jamie F. Collins* (2007) "Promoter Analysis of Rat Duodenal Genes Induced During Iron-Deficiency Reveals Enrichment of Conserved SP1 Binding Sites." BMC  Genomics, 8:420 
  19. Collins JF, Zihua Hu  (2007) "Microarray Analysis of Rat Duodenum during Iron- and Copper Deficiency." FASEB, 21: 934.
  20. 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 .
  21. 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 .
  22. 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 .
  23. 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 .
  24. Gallo SM, L Li, Zihua Hu , MS Halfon (2005) "REDfly: A Regulatory Element Database for Drosophila." Bioinformatics, 22:381-383 .
  25. 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 (2010) "Book review: Sequence Alignment: Methods, Models, Concepts, and Strategies." Am J Hum Biol. May;22(3): 427-428
  2. Zihua Hu (2004) "DNA Microarray and Data Analysis". In "Introduction to Bioinformatics", ZhengzhouUniversityPress, pp 153-174.
  3. Zihua Hu (2004) "Molecular Databases and Their Applications". In "Introduction to Bioinformatics", ZhengzhouUniversity Press, pp 75-110.
  4. Zihua Hu and Ping Liang (2004) "DNA and Protein Sequences Analysis". In "Introduction to Bioinformatics", ZhengzhouUniversityPress, pp 111-135.
  5. Zihua Hu and Wei Li (2004) "Elements of Statistics". In "Introduction to Bioinformatics", ZhengzhouUniversity Press, pp 221-261.
  6. 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 Congress of the International BioIron Society, Kyoto Japan, April 2007.
  7. Collins JF, Zihua Hu. Microarray Analysis of Rat Duodenum during Iron- and Copper Deficiency. Poster presented at Experimental Biology, WashingtonD.C. April 2007.
  8. 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.
  9. Collins JF and Zihua Hu(2006) Identification of Putative Transcriptional Regulatory Pathways Mediating the Genomic Response to Iron-deficiency in Rat Duodenum. Gastroenterology130:A540.
  10. 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.
  11. 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 International Copper Meeting. Alghero, Sardinia,Italy, October, 2006.
  12. 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

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.

Recent External Research Support:


1R01AI08556901A2   Schwartz (PI) - 09/2009 - 08/2011
Integration of Clinical, Genomic and Proteomic Data In HIV-1 using a Bioinformatic Approach

The overall goal of this study is the integration of the clinical, genomic and proteomic data derived from unique HIV-1 patient cohorts using bioinformaticsto yield a comprehensive database from which to predict patient outcomes and responses to therapy.

 

5R01AI028304-20  Murphy (PI) - 01/2005 - 12/2010
Development of a Vaccine for Moraxella Catarrhalis

The overall goal of this proposal is to evaluate proteins as vaccine antigens and to use a powerful genomics approach to identify and study potential vaccine antigens for M. catarrhalis.

 

American Heart Association - Yu (PI) - 01/2008 - 12/2011
The Role of Protein Arginine Methlation in Gene Expression

 

5R01DK074867-04 - Collins (PI) - 07/2007 - 06/2012
Molecular Mechanisms of Intestinal Metal Ion Transport During Iron-Deficiency

The overall goals are to determine the roles that Dmti and Atpya play in the induction of copper transport during iron-deprivation and to decipher the molecular mechanisms of induction of Dmti and Atpya during iron-deprivation.

 

5R01NS061856-02 - Feng (PI) - 12/2008 - 12/2013
Cellular Functions of Parkin

The overall goal is to improve our understanding of parkin and genes linked to early-onset Parkinson's disease, and to provide novel targets for the development of more effective therapies for Parkinson's disease.

Teaching:

Spring 2010 - Instructor for "Introduction of Bioinformatics and Computational Biology" BCH519 for graduate students

Spring 2009 - Instructor for "Introduction of Bioinformatics and Computational Biology" BCH519 for graduate students

Spring 2008 -  Instructor for "Introduction of Bioinformatics and Computational Biology" BCH519 for graduate students

Spring 2007 - Instructor for "Introduction of Bioinformatics and Computational Biology" BCH519 for graduate studentS