Bioinformatics

Services

• DNA Next Generation Sequencing (NGS) analysis
• Exome-Sequencing analysis
• ChIP-Seq analysis (narrow peaks or wider domains)
• RNA-Seq analysis
• DNA Methylation Sequencing analysis
• Ribo-Seq analysis
• Differential expression (RNA-Seq and DNA methylation)
• Variant discovery (DNA and RNA-Seq)
• Junction-based analysis of splicing events
• ENCODE correlations with NGS datasets
• The Cancer Genome Atlas (TCGA) NGS datasets
• Epigenetic signature discovery
• Transcription Factor Motif discovery
• Phosphorylation prediction
• microRNA target prediction
• Virus de novo Assembly
• Microarray analysis
• Biomarker panel design
• Pathway analysis
• Gene ontology analysis
• Proteomics analysis
• qPCR analysis
• Machine learning
• Custom scripts/software

Software Support

• Ingenuity Pathways
• MATLAB
• Bioinformatics public software (bowtie, bwa, MACS, RSEG, tophat, cufflinks, samtools, picard, IGV, GATK, GSEA, DAVID, hmmer, etc.)
• R, Python, Perl, Java and other programming languages

College of Medicine IT (Research Informatics)

COM IT offers a number of services that include consulting, web application development, programming, system and software installation and administration, high-performance computing resources and training. The team is committed to providing innovative solutions that exceed customer expectations while delivering first-class customer care.

Service Highlights

Technical Support and Consulting Services

COM IT provides consultation services for hardware/software procurement, application development, programming, and data-management options, and also supports a growing portfolio of custom and off-the-shelf applications.

Programming and Application Development

• Meeting with clients to analyze requirements for an application.
• Designing, testing and developing software solutions.
• Recommending upgrades and improvements for existing applications.
• Assisting with implementation of externally developed applications (vendor and open-source).
• Ensuring that applications function normally with maintenance and testing.
• Working with end users for support and training.
• Tuning software for maximum performance.
• Troubleshooting malfunctioning programs.

High Performance Computing Resources

High Performance Computing and enterprise-level storage provide researchers at Penn State College of Medicine the ability to quickly and efficiently process large amounts of data while allowing results to be accessed for the life of the research project. The system also allows researchers to work on multiple projects simultaneously while maintaining fast data transfer rates. HPC systems are utilized by preeminent universities and government agencies that depend on complex data analysis and applications.

System and Software Administration

• System and cluster hardware
• Compilers, libraries and middleware
• Broadly used applications

Application Highlights

• REDCap (Research Electronic Data Capture) is a tool for secure survey data capture and management.
• i2b2 (Informatics for Integrating Biology and the Bedside) is used for cohort identification through a database of de-identified patient information.
• StudyFinder is a searchable database of clinical research trials.

Contact Us

For details on COM IT, email Jason Hughes, Associate Chief Information Officer, at jhughes7@pennstatehealth.psu.edu or call 717-531-3727.