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.
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:
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.
1. Hu Z, Jiang K, Frank MB, Chen Y, Jarvis JN (2016) Complexity and Specificity of the Neutrophil Transcriptomes in Juvenile Idiopathic Arthritis. Sci Rep. 6:27453. doi: 10.1038/srep27453
2. Jiang H, Xu Z, Zhong P, Ren Y, Liang G, Schilling HA, Hu Z, Zhang Y, Wang X, Chen S, Yan Z, and Feng J (2015) Cell cycle and p53 gate the direct conversion of human fibroblasts to dopaminergic neurons. Nature Communication. Dec 7;6:10100. doi: 10.1038/ncomms10100
3. Sapkota D, Chintala H, Wu F, Fliesler SJ, Hu Z, Mu X (2014) Onecut1 and Onecut2 redundantly regulate multiple retinal cell fates during development. PNAS.111(39):E4086-95.
4. Li R, Wu F, Ruonala R, Sapkota D, Hu Z, Mu X (2014) Isl1 and Pou4f2 form a complex to regulate target genes in developing retinal ganglion cells. PLoS One.18;9(3):e92105.
5. Kuo SM, Chan WC, Hu Z (2014) Wild-type and IL10-null mice have differential colonic epithelial gene expression responses to dietary supplementation with synbiotic Bifidobacterium animalis subspecies lactis and inulin. J Nutr.144 (3):245-51.
6. Jiang K, Hu Z, Chen Y, Jarvis JN (2014) A176: deep sequencing reveals differential small RNA expression in serum exosomes of children with juvenile idiopathic arthritis. Arthritis Rheumatol. 66 Suppl 11:S230.
7. Li XM, Yan QY, Xie SQ, Hu W, Yu YH, Hu Z* (2013) Gut Microbiota Contributes to the Growth of Fast-growing Transgenic Common Carp (Cyprinus carpio L.). PLoS One. 8(5): e64577.
8. Patel M, Hu Z, Bard J, Jamison J, Cai Q, Hu BH (2013) Transcriptome Characterization by RNA-Seq Reveals the Involvement of the Complement Components in Noise-Traumatized Rat Cochleae. Neuroscience. May 29.
9. Patel M, Cai Q, Ding D, Salvi R, Hu Z, Hu BH (2013) The miR-183/Taok1 Target Pair Is Implicated in Cochlear Responses to Acoustic Trauma. PLoS One. 8(3):e58471
10. Pan YZ, Zhou A, Hu Z, Yu AM (2013) Small Nucleolar RNA-Derived Microrna hsa-Mir-1291 Modulates Cellular Drug Disposition Through Direct Targeting of ABC Transporter ABCC1. Drug Metab Dispos. May 16
11. 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.
12. 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:e32957
13. 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.
14. 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.
15. Milliman EJ, Hu Z, Yu MC (2012) Genomic insights of protein arginine methyltransferase Hmt1 binding reveals novel regulatory functions. BMC Genomics. 13(1):728
16. Hu Z*, Bruno A (2011) The influence of 3’UTRs on microRNA function inferred from human SNP data. Comparative and Functional Genomics.
17. Li X, Pan YZ, Seigel GM, Hu Z, Huang M, Yu AM (2011) Breast cancer resistance protein BCRP/ABCG2 regulatory microRNAs (hsa-miR-328, -519c and -520h) and their differential expression in stem-like ABCG2+ cancer cells. Biochem Pharmacol. 15;81(6):783-92.
18. Hu Z*, Gallo S (2010) Identification of interacting transcription factors controlling gene expression in human tissues. BMC Genomics;11:49.
19. Hu Z*, 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. 299(5):C930-8.
20. Aalinkeel R, Hu Z, Nair BB, Sykes DE, Reynolds JL, Mahajan SD, Schwartz SA (2010) Genomic analysis highlights the role of the JAK-STAT signaling in the anti-proliferative effects of dietary flavonoid—Ashwagandha’in prostate cancer cells Evidence-Based Complementary and Alternative Medicine 7 (2), 177-187
21. Hu Z* (2009) Insight into microRNA regulation by analyzing the characteristics of their targets in humans. BMC Genomics;10:594.
22. Mahajan SD, Aalinkeel R, Reynolds JL, Nair BB, Sykes DE, Hu Z, 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.
23. Lindemann MJ, Hu Z, 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.
24. Ananthi J. Asirvatham, Christopher J. Gregorie, Hu Z, 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.
25. Ruckdeschel E, Kirkham C, Lesse AJ, Hu Z, Murphy TF (2008) Mining the Moraxella catarrhalis Genome: Identification of Potential Vaccine Antigens Expressed during Human Infection. Infect Immun; 76(4):1599-1607.
26. James F. Collins, Hu Z, 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.
27. Ravikumar A, Hu Z, Balakrishnan B, Donald ES, Reynolds JL, Mahajan SD, Schwartz SA (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.
28. Bindukumar B, SD Mahajan, JL Reynolds, Hu Z, 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.
29. Hu Z*, Hu B, Collins JF (2007) Prediction of Synergistic Transcription Factors by Function Conservation. Genome Biology, 8:R257.
30. Hu Z*, 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
31. Collins JF, Hu Z (2007) Microarray Analysis of Rat Duodenum during Iron- and Copper Deficiency. FASBE21: 934.
32. Hu Z*, Wilsky GR (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.
33. Shen F, Hu Z, Goswami J, Gaffen SL (2006) Identification of Common Transcriptional Regulatory Elements in Interleukin-17 Target Genes. J Biol Chem. 281:24138-24148.
34. Mahajan SD, Hu Z, Reynolds JL, Aalinkeel R, Schwartz SA, Nair MPN (2006) Methamphetamine Modulates Gene Expression Patterns in Monocyte Derived Mature Dendritic Cells: Implications for HIV-1 Pathogenesis. Mol Diagn Ther. 10:257-269.
35. Willsky GR, Chi L-H, Liang Y, Gaile DP, Hu Z, Crans DC (2006) Diabetes Altered Gene Expression in Rat Skeletal Muscle Corrected by Oral Administration of Vanadyl Sulfate. Physiological Genomics,26:192-201.
36. Gallo SM, Li L, Hu Z, Halfon MS (2005) REDfly: A Regulatory Element Database for Drosophila. Bioinformatics, 22:381-383.
37. Guo M, Rupe M, Danilevskay O, Yang X, Hu Z (2003) Genome-wide mRNA Profiling Reveals Heterochronic Allelic Variation and a New Imprinted Gene in Hybrid Maize Endosperm. Plant J, 36:30-44.
38. Hu Z, Poulton JP (1999) Molecular Analysis of (R)-(+)-Mandelonitrile Lyase Microheterogeneity in Black Cherry. Plant Physiology 119: 1535-1546.
39. Hu Z, Poulton JP (1997) Sequencing, Genomic Organization and Preliminary Promoter Analysis of a Black Cherry (Prunus serotina) (R)-(+)-Mandelonitrile Lyase Gene. Plant Physiology 115: 1359-1369
Source: NIH 2R01EY019949 Period: 09/2015 – 08/2019
Title: ER Stress and Diabetic Retinopathy
PI: Xin Zhang
Major Goals: Diabetic retinopathy (DR), a major complication of diabetes, is a leading cause of vision impairment and loss in the working age population. The goals are to delineate the role of endoplasmic reticulum (ER) stress in the development of retinal vascular pathology in diabetes, and to test the therapeutic potential of a novel protective agent in counteracting ER stress and inflammatory damage of retinal cells in DR. The realization of these goals is anticipated to identify a novel mechanism underpinning the retinal complications of diabetes and pave the way for new therapies to prevent/treat this sight-threatening disease
Source: NIH (NCI) 1U01CA175315 Period: 04/2014 – 03/2019
Title: microRNA-1291 IN regulation of xenobiotic disposition and cell differentiation
PI: Aiming Yu
Major Goals: The study is to delineate the mechanistic functions of miR-1291 in the regulation of drug disposition and endobiotics homeostasis and to define its roles and molecular in the control of cancer cell proliferation, invasion, and tumor progression processes. The final goal is to establish the effectiveness and safety profiles of miR-1291 therapeutics in clinically relevant animal models
Source: NIH R01 AI061580 06A1 Period: 04/2012 – 03/2017
Title: Regulation of RNA editing in Trypanosoma Brucei
PI: Laurie Read
Major Goals: To reveal the molecular mechanisms of RNA
editing in kinetoplastid parasites. The RNA editing event is unique
to kinetoplastids and absent from their human hosts
Source: NIH 1R21HD075218 Period: 04/2014 – 03/2016
Title: Trophoblasts and Inflammation: An Epigenetic Approach
PI: Jim Jarvis
Major Goals: To characterize genome-wide methylation patterns in term chorionic trophoblasts in an in vitro model of inflammation using two complementary, sequencing-based methods, and to perform genome-wide analysis of the trophoblast transcriptome in this same model, examining expressed genes, splice variants, and non-coding transcripts that may affect the physiologic response of the trophoblast to inflammation
Source: NIH 1R01EY020545 Period: 04/2011 – 03/2016
Title: Interaction of Isl1 and Pou4f2 in retinal development
PI: Xiuqiqn Mu
Major Goals: The overall goal is to understand how two transcription factors, Isl1 and Pou4f2, interact and regulate gene expression during the development of retinal ganglion cells. This will further our understanding of the structure and logic of the gene regulatory network underlying the specification and differentiation of retinal ganglion cells which are critical for vision.
Source: NSF Period: 03/2011 – 02/2015
Title: The role of protein arginine methylation in the co-transcriptional recruitment of pre-mRNA splicing factors
PI: Michael Yu
Major Goals: The overall goals of this project are to examine the mechanisms by which protein arginine methylation modulates the co-transcriptional recruitment of splicing factors in the simple eukaryotic model organism Saccharomyces cerevisiae. A combination of molecular biology, biochemistry, proteomic, and genomic methodologies will be used.
Source: NIH 1R01AI0855690 Period: 09/2009 – 08/2011
Title: Integration of Clinical, Genomic and Proteomic Data In HIV-1 using a Bioinformatic Approach
PI: Stanley Schwartz
Major Goals: The overall goal of this study is the integration of the clinical, genomic and proteomic data derived from unique HIV-1 patient cohorts using bioinformatics to yield a comprehensive database from which to predict patient outcomes and responses to therapy.
Source: NIH 5R01AI028304 Period: 01/2005 – 12/2010
Title: Development of a Vaccine for Moraxella Catarrhalis
Major Goals: 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.
Source: NIH Period: 01/2011 – 12/2011
Title: Pathogenesis of Haemophilus Influenza Infection in Copd
Major Goals: Persistence of nontypeable Haemophilus influenzae in the lower airways of adults with chronic obstructive pulmonary disease (COPD) causes airway inflammation and impaired pulmonary function. The goal of this proposal is to use state of the art methods to investigate how NTHI persists and the consequences of its persistence. The results will reveal new ways to eradicate persistent NTHI and have great potential for novel discoveries to prolong and improve the lives of people with COPD
Source: American Heart Association Period: 01/2008 – 12/2011
Title: The Role of Protein Arginine Methlation in Gene Expression
Major Goals: The proposed studies are to provide valuable information for the elucidation of the role of protein arginine methylation in the control of gene expression relevant to their function in maintaining genome stability.
Source: RPCI Period: 09/2009 – 09/2019
Title: MicroRNA Targets in Immune Genes and the Dicer/Argonaute and ARE Machinery Components
Source: RPCI Period: 09/2010 – 09/2013
Title: Medical and biological data analysis and mining
Major Goal: The overall goal of this grant is to use computational and bioinformatics approaches to improve the understanding of cancer using data from both medical and biomedical research
Source: NIH 5R01DK074867 Period: 07/2007 – 06/2012
Title: Molecular Mechanisms of Intestinal Metal Ion Transport during Iron-Deficiency
PI: James Collin
Major Goals: 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.
Source: NSF Period: 07/2004 – 07/2006
Title: Genome Sequencing of Plant-associated Azospirirllum brasilense
PI: Matthew Koffas
Major Goals: The overall goal is to complete genome sequencing of A. brasilense in order to gain insights into the biology of plant-microbe associations and the biochemistry of biosynthetic pathways for future advances in its agronomic and industrial applications.
Source: University at Buffalo Period: 09/2008 – 08/2009
Title: MicroRNA Regulation of ABC Membrane transporters
PI: Aiming Yu
Major Goals: The overall goal of this study is to understand the microRNA regulation on ABC membrane transporter related genes.
Source: General Mills Period: 04/2006 – 03/2008
Title: Effect of Dietary yogurt and Fiber on the Management of Intestinal Inflammation
PI: Shiu-Ming Kuo
Major Goals: The overall goal is to use dietary factors to modulate inflammatory responses as a mean to manage gastrointestinal diseases
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