Core Director: Dr. Kurt Zhang, Picture and Address from ND INBRE Website
Summary of Dr. Zhang
Our research is focused on elucidating the molecular and genetic mechanisms underlying pathological processes using genomic studies. We employ the cutting-edge high-throughput technology such as next-generation sequencing, proteomics and microarray chips to conduct systems biology studies. A major effort in our lab has been devoted to develop advanced computer algorithms and statistical methods for bioinformatics research.
Our research areas include:
Cancer genomics: identification of cancer biomarkers and development of new genetic tests for early diagnosis and prognosis.
Gene regulatory networks: understanding the gene-gene interactions in development and disease progression.
Clinical trials: conducting multiple pre-clinical and clinical trials for cancer and infectious diseases.
Transcriptome assembly: development of a novel de novo assembly algorithm for RNA-Seq data.
Link to CV, can be found at the MPH Website.
Introduction: 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.
Mission: The INBRE Bioinformatics Support Service 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.
Dell PowerEdge: The Bioinformatic Core 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 computation of 64 processes simultaneously. This server has enabled the core to fulfill many of the required tasks for bioinformatics research and education. The R910 is a single-node server and a major advantage of R910 is that it has a large shared memory (500 GB) that allows development of computational algorithms with a large data structure.
Dell Cluster Server: The Dell PowerEdge R910 server was becoming a limiting factor for meeting the computational requirements for the fast-growing area of genomic data-sets. To compliment and extend bioinformatic capability, a Dell Cluster Server was added to the Bioinformatic Core facility. The Dell Cluster Server consists of: One Dell Blade Server M1000E PowerEdge; Sixteen PowerEdge M520 Blade Server; and, One PowerConnect M8024-K Managed Switch.
UND and ND University System (NDUS) Computing: For advice and access to high performance needs, Dr. Zhang is a member of the UND Data Vortex Interest Group and the UND Data Management Committee.
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. 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 ND INBRE 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 Multiple Principal Investigator. Investigators are welcome to discuss such opportunities for collaboration.