Research Programs: Bioinformatics Core

Bioinformatics is an emerging interdisciplinary field that utilizes advanced statistical and IT technology for gathering, analyzing, storing, and disseminating biological data. The rapid advancement of high-throughput technology, such as genomics and proteomics, has required bioinformatics to play an increasingly important role in various areas of molecular biology including macromolecule structure, gene network and population genetics.

The INBRE Bioinformatics Core Facility provides biomedical researchers consultative advice on data processing and analysis for various types of data, including next generation sequencing data, genome-wide association (GWAS), epigenomics, global gene expression, DNA copy number variation, and microRNA. The facility also provides, or attempts to arrange, consultative services for investigators needing support in biostatistics for clinical trial design, power calculations, statistical analysis for risk assessment, disease early detection, prevention, prognosis, and interactions with multiple factors. The ND INBRE Bioinformatics Core maintains a strong collaborative relationship with Computer Sciences at UND. The facility also provides training for undergraduate students, graduate students and post-doctoral fellows in bioinformatics technology.

Computing Equipment

The facility is equipped with a Dell PowerEdge R910 4U rack server that has four Intel Xeon X7550 CPUs and 512 GB RAM. This R910 server allows parallel computing of 64 processes simultaneously. Additional computing power is obtained through our partnership with UND Computational Research Center for their cluster computer.

Software Development

Various software tools have been developed in this facility. All software packages are available to academic users. If you wish to use the software for commercial purpose, please contact Dr. Kurt Zhang at ke.zhang@med.und.edu.

  • Gene set enrichment analysis for longitudinal expression profiles
  • DNA segmentation using a novel nonparametric method
  • Tumor subtype classification using a non-negative matrix decomposition method for DNA copy numbers
  • Tumor subtype classification using a hidden Markov model for DNA copy numbers
  • Biomarker cutoff determination for survival data

Fee For Service

Consultation: The ND INBRE will support from internal resources the limited hours of consultation costs that are necessary for investigators to propose high quality research involving bioinformatics. In no instance should such consultative needs exceed 4 hours. This consultative services is aimed at three core areas: 1. The discussion of, and examination of, protocols prior to submission to commercial and other outside agencies for the generation of data that will require subsequent or cost-included bioinformatic analysis; 2. The discussion and examination of protocols involving bioinformatics proposed in investigator-initiated intramural and extramural grants and contracts prior to submission to the funding agency; and, 3. The examination and evaluation of bioinformatic data sets generated by investigators prior to establishment of the ND INBRE core facility and an estimate of the costs of subsequent data analysis.

Data Analysis: Investigators requiring data analysis by the ND INBRE core will be charged at the rate of $89.00 per hour of analysis time. Investigators proposing the usage of the ND INBRE Bioinformatics Core on intramural and extramural grants and contracts should use this rate on the applications. A letter from the Director of the Bioinformatics Core and a current biographical sketch will be provided to investigators requesting core usage. It is expected that all investigators will have used the ND INBRE Bioinformatic Core consultative services to define the need and degree of such services prior to including bioinformatics services on their applications.

Direct Collaboration: The Director of the ND INBRE Bioinformatics Core is not engaged full- time in core activities and does have independent time available for direct effort on extramural research grants as a Principal or Multiple Principal Investigator. Investigators are welcome to discuss such opportunities for collaboration.

longiGSEA

Gene set enrichment analysis for longitudinal microarray experiments.
Version: 1.0
Depends: R (= 2.7.0)

Published: 2010-12-21
Author: Kurt Zhang, Kaitlin Clarke, Haiyan Wang
Maintainer: Kurt Zhang, Kaitlin Clarke
License: GPL-3
URL: N/A

Download longIGSEA
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Urotsatransformants

Core Director

Kurt Zhang, PhD
Assistant Professor
Department of Pathology
University of North Dakota School of Medicine
501 North Columbia Road Room 3573
Grand Forks, ND 58202-9037
Office phone: (701) 777-0389
Department FAX: (701) 777-3108
Email: ke.zhang@med.und.edu