RISS Projects & Activities

 
To best address the needs of the University's research communities, RISS has undertook a multi-pronged approach, providing both the human infrastructure with informatics analysts who work closely with researchers as well as developing the cyber-infrastructure by implementing leading edge software, analytical data resources and by promoting best practices in data management, analysis and project management.
 

1. Infrastructure projects supported through RISS

 

Galaxy

The Galaxy analytical framework is an open source software application designed to support bioinformatics and genomics data analysis.  Galaxy implementation at MSI was led by RISS Program Director, Anne Lamblin,  with a competitive award from the Minnesota Partnership Infrastructure program.  Galaxy continued support and maintenance is provided by the Application Development group and the IOUS staff at MSI.  This infrastructure effort is to create a user-friendly  environment for bioinformatics while yet offering leading edge analytical functions and best practices in metadata capture. See more at: http://galaxy.msi.umn.edu/home or log in to use Galaxy at: https://galaxy.msi.umn.edu

 

Galaxy-P

Building on the success of the Galaxy framework and its wide use by genomics researchers, the University of Minnesota is extending the genomics framework to proteomics by integrating tools for mass spectrometry (MS) proteomics research.  The project is named Galaxy-P.   RISS Program Director worked with Dr. Tim Griffin in the development of the  Galaxy-P proposal.  Software development is done by MSI AppDev group. The Galaxy-P project is funded through the National Science Foundation (Award 1147079).

 

UMGC Illumina processing pipeline

UMGC, the University of Minnesota Genomics Center, generates Terabytes worth of Illumina HiSeq data output on a routine basis ( ~10days).  All pre-processing of the data before it is released to the researcher is done at MSI.  In collaboration with the MSI Application Development group and the UMGC, the RISS  team coordinated the development of a pipeline to automate that complete process, including Illumina run statistics, demultiplexing and QA/QC.  Data is automatically delivered to the researcher MSI account and accessible through Galaxy, ready for analysis.  

 

UMGC

 

2. Examples of projects supported through RISS

(sorted by service type, department and investigator)
Project 
Investigator
Dept
 Type of service
Statistical genetics software development  Da, Yang Animal Sciences Analysis
Leukotrienes-induced gene expression study Hertzel, Ann BMBB Analysis
Genomic Signatures of Colorectal -Cancer novel fusion oncogenes in a clinically relevant set of human colorectal cancers Cormier, Robert Cancer Center , Duluth Analysis
Comparative analysis of potato genome for SNP variant identification Tong, Cindy Horticultural Sciences Analysis
Targeting the aberrant androgen receptor in advanced treatment resistant prostate cancer Dehm, Scott Lab Medicine and Pathology Analysis
Study of the Androgene receptor gene structure alterations and prostate cancer progression Dehm, Scott Lab Medicine and Pathology Analysis
Transposon genetic screen to study acute lymphoblastic leukemia Farrar, Michael Lab Medicine and Pathology Analysis
 Diabetes research Gross, Myron Lab Medicine and Pathology Analysis
 Ataxia research Thyagarjan, Bahrat Lab Medicine and Pathology Analysis
CLIA diagnostic genetic test development and support Thyagarjan, Bahrat Lab Medicine and Pathology Analysis
Gene expression signature of corneal limbal stem cell Ching, Yuan Ophtalmology Analysis
Molecular epidemiology of pediatric germ cell tumors Poynter, Jenny Pediatrics Epidemiology Analysis
Study of PAX2 role in renal coloboma syndrome  Schimmenti, Lisa Pediatrics Opthalmology Analysis
Analysis of barley and soybean rust fungus Rouse, Matthew Plant Pathology Analysis
Medicago HapMap project Young, Nevin Plant Pathology Analysis
Identification of long non-coding RNAs Kikyo, Nobuaki Stem Cell Institute Analysis
Chicken viral & bacterial metagenomics Cardona, Carol Veterinary Sciences Analysis
Molecular basis of interactions between rice fungi and wild-rice  Samac, Debby Plant Biology Analysis 
       
Chinese Hamster genome assembly and analysis Hu, Wei-Shou Cell Engineering Analysis and training
Molecular basis of the Virginia opossum immunity to snake venom. Jansa, Sharon Ecology, Evolution and Behavior Analysis and training
       
Dual-label proteomics quantitation software development Arriaga, Edgar Chemistry Application development 
Galaxy-P: Using Galaxy framework to support Proteomics data analysis Griffin, Tim BMBB Application development
Personalized tumor vaccine immunotherapy Largaespada, David  (Ohlfest, John) MCBB Application development 
Automated Illumina data output processing Beckman, Kenny UM Genomics Center Application development 
       
Gravitational Regulation of Osteoblast Genomics and Metabolism Hammer, Bruce Center for Magnetic Resonnance Consulting
CTSI Blazar, Bruce;  Delaney, Connie Medicine Consulting
Bioinformatics Classes development Springer, Nathan Plant Biology & CBS Consulting
       
Applying data processing techniques in egyptian papyrology Fortson, Lucy Physics Data management & discovery
       
Private sector company     External Sale Contract - Infrastructure, Analysis, Training
       
Regulation of cell cycle progression in cancer cells (project consultation) Cornell, Greg  Molecular Cell Biology Project consultation
Genomic characterization of Pennycress (Thalaspi arvensi) for the development of a sustainable weed management system and biodiesel feedstock (Project consultation) Marks, david Plant Biology Project consultation
       
Assembly and annotation of Thiomargarita and Chamaesiphon genomes (proposal consultation) Bailey, Jake Earth Sciences Proposal consultation
Prezygotic interspecific reproductive barriers in Nicotiana (proposal preparation) Smith, Alan Horticultural sciences Proposal consultation
Dissecting the regulatory crosstalk mechanisms between plasmids and their host chromosomes – proposal preparation Johnson, Tim Veterinary and Biomedical Sciences Proposal consultation
       
Keck foundation - Cell Mass Spectrometer Arriaga, Edgar Chemistry Proposal development
NIH-Streptococcus faecalis protein Functional annotation Dunny, Gary Microbiology Proposal development (U19)
Galaxy-P: Using Galaxy framework to support Proteomics data analysis Griffin, Tim BMBB Proposal development
Antimicrobial peptide application in food safety Kaznessis , Yiannis Chemical Engineering and Material Sciences Proposal development 
NIH Metabolomics Center Nelsestuen, Gary BMBB Proposal development (U19)
       
Hepatic gene expression changes associated with residual feed intake in beef cattle. Fahrenkrug, Scott Animal Science Training

 


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