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Bioinformatics Core Facility

Overview

The Bioinformatics Core Facility serves as a centralized resource for providing expert and timely bioinformatics consulting, analysis, collaborative research, management, and training solutions for high-throughput data. The data includes different kinds of “omics” data (e.g., genomics, transcriptomics, epigenomes, proteomics, metabolomics, metagenomics data), which are generated from a variety of platforms such as PCR, microarray, NGS, mass-spec, and so on. The core provides high-level expertise in bioinformatics, ensuring the support needed to design, conduct, analyze, interpret and manage results requiring or facilitated by informatics applications. Bioinformatics support will be integrated into all phases of basic, clinical and translational research through a coordinated program of bioinformatics consultation and analysis.

The Bioinformatics Core Facility aims to build and maintain as an infrastructure resource that enables the application of strong bioinformatics solutions with a measurable impact on the ability of JABSOM and UH investigators to both publish their work and obtain new funding.

Services

The Bioinformatics Core Facility provides the following services in hopes of building and maintaining an infrastructure that enables the applications of strong informatics solutions:

  1. Consultation
  2. Data Analysis
  3. Grant Support
  4. Data Management Service
  5. Collaborative Research

Consultation

Experimental Design and Power Calculations – We highly encourage you to consult our bioinformatician prior to experiments to find a solution that fits your needs and budget. We will help design your experiments to obtain maximum leverage and perform data quality control checks for high-throughput data projects.

Liaison with vendors: We will help identify the right product to ensure the quality of your research.

Data Analysis

  • Next Generation Sequence Analysis
    • Assembly and gene annotation
    • DNA-Seq
    • RNA-Seq including fusion gene and LncRNA
    • Small RNA-Seq
    • Chip-Seq
    • Target-Seq
    • Meth-Seq
    • Metagenomics
  • Microarray data analysis
    • Gene expression
    • Exon array for alternative splicing
    • SNP array, GWIS
    • miRNA array
    • DNA methylation array
    • CNV
  • Proteomics data and Protein array
    • Protein mass-spec data for protein expression and interaction
    • Phosphor-screen
    • Glycol-screen
    • PTM (post translation modicication) Profilling
  • Metobolomics data analysis
      Lipidomics
    • Sugar profiling
    • Entire metabolomics data analysis
  • Multivariate biomarker identification and classification
    • Feature selection algorithms
    • Classification algorithms
  • Gene pattern, function analysis, systems biology
    • Gene and sample correlation and clustering analysis
    • Gene enrichment analysis
    • Gene ontology and pathway analysis
    • Gene network analysis
    • Integrative "omics" data analysis
  • Image data analysis
  • Single Cell Sequencing
  • Nanostring Data Analysis

Grant Support

We will provide hardware and software support for UH researchers who plan to conduct preliminary data analysis for hypothesis development and testing as part of grant proposal writing. We will provide necessary guidance to include computational biological methods to analyze data in your research analysis plan. Letters of support for your grant proposal can be prepared upon request.

Data Management Service

We will provide data management services and develop a web-based database for collection, storage, integration, and management of clinical data and scientific research data.

Collaborative Research

We are involved in collaborative research of several principal investigators from different UH departments and campuses. We perform bioinformatics data analysis by running routine bioinformatics applications and custom programs developed specifically to fulfill our research objectives.

Members


Youping Deng, Ph.D. | Professor and Director, Bioinformatics Core Facility
Email: dengy@hawaii.edu
Phone: (808) 692-1664


Vedbar Khadka, Ph.D. | Assistant Professor
Email: vedbar@hawaii.edu
Phone: (808) 692-1462


Yujia Qin, Ph.D. | Bioinformatician
Email: yqin@hawaii.edu


Joshua Burkhart, Ph.D. | Post-Doctoral Researcher
Email: jgburk@hawaii.edu


Yuanyuan Fu, Ph.D. | Post-Doctoral Researcher
Email: fuy@hawaii.edu
Phone: (808) 692-1529


Mayumi Jijiwa, M.D., Ph.D. | Post-Doctoral Researcher
Email: jijiwa@hawaii.edu
Phone: (808) 692-1531


Masaki Nasu, Ph.D. | Post-Doctoral Researcher
Email: mnasu@hawaii.edu
Phone: (808) 692-1670


Sudhir Rai, Ph.D. | Post-Doctoral Researcher
Email: raisk21@hawaii.edu


Shaoqiu Chen, B.S. | Ph.D. Graduate Research Assistant
Email: shaoqiu@hawaii.edu


Yu Chen | Ph.D. Graduate Research Assistant
Email: yuchen8@hawaii.edu


Ting Gong, M.S. | Ph.D. Graduate Research Assistant
Email: tgong@hawaii.edu
Phone: (808) 692-1613


Zitong Gao, M.S. | Graduate Research Assistant
Email: zitong@hawaii.edu


Isam B. Mohd Ibrahim | Graduate Research Assistant
Email: isambmi@hawaii.edu


Emory Zitello | Graduate Research Assistant
Email: ez9@hawaii.edu


Hua Yang, MBA | Manager
Email: yanghua@hawaii.edu
Phone: (808) 692-1529



Seminars/Workshops

We offer seminars workshops depending on the interest of our research community. Our faculty members have mentored visiting scholars, students, and trainees, and have served as thesis and dissertation committee members of graduate students from across campus.

Note: For upcoming seminars or workshops, please contact us for details.

Publications

If you utilize the Bioinformatics Core Facility in publications, abstracts, posters, and oral presentations, please insert the following acknowledgement as a result from the services provided to you:

"XXX(Individual initials) was(were) partially supported by grant U54MD007584 from the National Institute on Minority Health and Health Disparities as well as grants P20GM103466 and P30GM114737 from the National Institute of General Medical Sciences from the National Institutes of Health. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH."



List of Selected Publications


  • Dye CK, Corley MJ, Li D, Khadka VS, Mitchell BI, Sultana R, Lum-Jones A, Shikuma CM, Ndhlovu LC, Maunakea AK. Comparative DNA methylomic analyses reveal potential origins of novel epigenetic biomarkers of insulin resistance in monocytes from virally suppressed HIV infected adults. Clinical Epigenetics. 2019 Jul;11(1):95. doi:doi.org/10.1186/s13148-019-0694-1. PubMed PMID: 31253200; PubMed Central PMCID: PMC6599380.

  • Sasuclark AR, Khadka VS, Pitts MW. Cell-type specific analysis of selenium-related genes in brain. Antioxidants. 2019 May;8(5):120. doi:10.3390/antiox8050120. PubMed PMID: 31060314; PubMed Central PMCID: PMC6562762.

  • Deng Y, Zhu Y, Wang H, Khadka VS, Hu L, Ai J, Dou Y, Li Y, Dai S, Mason CE, Wang Y, Jia W, Zhang J, Huang G, Jiang B. A ratio-based method to identify true biomarkers by normalizing circulating ncRNA sequencing and quantitative PCR data. Analytical Chemistry. 2019 May 21;91(10):6746-6753. doi:10.1021/acs.analchem.9b00821. PubMed PMID: 31002238.

  • Fang R, Zhu Y, Khadka VS, Zhang F, Jiang B, Deng Y. The evaluation of serum biomarkers for non-small cell lung cancer (NSCLC) diagnosis. Frontiers in Physiology. 2018 Nov;9(1710):1-6. doi:10.3389/fphys.2018.01710. PubMed PMID: 30555348; PubMed Central PMCID: PMC6281717.

  • Sah N, Kuehu DL, Khadka VS, Deng Y, Peplowska K, Jha R, Mishra B. RNA sequencing-based analysis of the laying hen uterus revealed the novel genes and biological pathways involved in the eggshell biomineralization. Scientific Reports. 2018 Nov;2018(8):1-12. doi:10.1038/s41598-018-35203-y. PubMed PMID: 30443032; PubMed Central PMCID: PMC6237962.

Bioinformatics Resources

Bioinformatics Data Repositories and Tools

  • NCBI GenBank
    Database of nucleotide and protein sequence data

  • EMBL-EBI
    Database of nucleotide and protein sequence data

  • DDBJ
    Database of nucleotide and protein sequence data

  • Pfam
    Database of protein families

  • ArrayExpress
    Database of high-throughput functional genomics data

  • NCBI CDD
    Conserved Domain Database is a protein annotation resource

  • MGI: Mouse Genome Informatics
    Database and bioinformatics resource on the genetics, genomics, and biology of mouse

  • TIGER
    Database of tissue-specific gene expression and regulation data

  • Cancer Genome Anatomy Project
    Database of normal, pre-cancerous and cancerous genomes

  • RCSB Protein Databank
    Repository of 3D structures of large biological molecules, including proteins and nucleic acids

  • NCBI GEO
    Repository of functional genomics (both array- and sequence-based) data

  • ENCODE
    Repository of Encyclopedia of DNA Elements (ENCODE) data

  • ExPASy
    Resource portal includes databases and tools in different areas of life sciences including proteomics, genomics, structural bioinformatics, systems biology, phylogeny, population genetics, transcriptomics, drug design, and others.

  • TCGA
    The cancer genome atlas data portal

  • Smart
    Tool for protein domains identification and analysis

  • ElliPro: Antibody Epitope Prediction
    Tool to predict and analyze immune epitopes

  • QuickGo
    Tool for gene ontology searching

Computational Resources

  • In-House
    • QHS Beowulf Cluster
      • Consists of 3 nodes and two nodes of 14 Cores and 256 GB RAM each.
  • On-Campus
 

Software Resources

  • Array Suite
  • Ingenuity Pathway Analysis
    •    
  • CLC Genomic Workbench 9
  • CLC Drug Discovery Workbench 3
Bioinformatics Core

University of Hawaiʻi John A. Burns School of Medicine
651 Ilalo Street
Biological Sciences Building, Suite 222
Honolulu, HI 96813

Director: Youping Deng, Ph.D.
Phone: (808) 692-1664
Email: dengy@hawaii.edu (Youping Deng),
or vedbar@hawaii.edu (Vedbar Khadka)

Manoa

651 Ilalo Street, Medical Education Building, Suite 411, Honolulu, HI 96813

Phone: 808.692.1840 / Email: dqhs@hawaii.edu

JABSOM

© Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine