Bioinformatics Shared Resource

The Department of Medicine (DOM) Bioinformatics Shared Resource, part of the Genomics Research Center (GRC), provides computational analysis and support services for biomedical data including next-generation sequencing. Our mission is to accelerate scientific discoveries by guiding experimental design, performing robust data quality assessment, carrying out comprehensive computational analyses, and integrating multi-modal biomedical datasets to provide insights into biological function and mechanisms of disease. We contribute to all aspects of the research cycle, including generating ideas and preliminary results for grant applications; performing data management, analysis, and interpretation; and preparing manuscripts for publication.

We generally support two types of analyses through this program, including both basic/standardized and advanced/customized analyses. These are described in more detail below, and while basic/standardized analyses will always be supported, support for advanced/customized analyses will be dependent on the specific request. 

1. Basic/Standardized Analyses
   Examples include quality assessment and processing of the most common types of genomics data (e.g., DNA-seq, RNA-seq, scRNA-seq, ATAC-seq, ChIP-seq, spatial transcriptomics) using established computational pipelines.
2. Advanced/Customized Analyses
   Such analyses typically involve integration of multiple types of genomics data, development of new computational workflows, and mining of publicly available data.
   
   The DOM Bioinformatics Shared Resource is committed to providing bioinformatic support to mentored trainees and faculty performing excellent science who do not have current funding available to cover those activities. The program was implemented on July 1, 2025. Resource staff includes Dr. Hannah Aichelman, PhD (Genomics Research Center) along with support from other GRC bioinformaticians. Access to the Shared Resource Bioinformatics support is provided through a REDCap tool, and trainees should please include their mentor’s name in the request. Resource staff will additionally host office hours, and investigators can schedule 30-minute meeting slots in advance through a Microsoft Bookings tool.

In order to protect bioinformatician’s time during busy periods, the recommended deadline for applications for meetings/grants is 4-8 weeks prior, however depending on demand or nature of the project we realize that this may not be feasible and so if time is an issue this will be addressed at the time of the consultation. Please visit NIH standard deadlines for important dates and remember ORPA’s 5 business days lead time.

Request Bioinformatics Support Schedule Office Hours

Project Initiation Template & First Meeting Expectations

To help ensure projects are appropriately scoped, prioritized, and completed on schedule, all new collaborations begin with a project initiation discussion.

Prior to the first consultation, investigators may be asked to provide background information regarding their research objectives, data sources, anticipated deliverables, timelines, and key research questions. This information is documented using the Bioinformatics Shared Resource Project Initiation Template.

The project initiation process helps:

• Clearly define project goals and expected outcomes
• Identify available datasets and technical considerations
• Establish an analysis plan and timeline
• Clarify deliverables and investigator responsibilities
• Track outstanding items needed to move the project forward
• Improve communication and project management throughout the collaboration

What to Expect During the Initial Meeting

During the initial consultation, the Bioinformatics Shared Resource team will work with investigators to:

• Review the scientific objectives and research questions
• Discuss available data and data quality considerations
• Clarify study design and analysis needs
• Identify required approvals, data access, or technical dependencies
• Establish expected timelines and milestones
• Define project deliverables and next steps

Following the meeting, a project initiation document will be finalized and used as a shared project roadmap throughout the collaboration.

Questions?

If you have any questions related to this program, please directly reach out to Laura Calvi Laura_Calvi@URM.Rochester.edu, Valentina Kutyifa Valentina_Kutyifa@urmc.rochester.edu, or Stefanie Fingler Stefanie_Fingler@URMC.Rochester.edu.

Other Useful Resources

1. The Genomics Research Center offers hands-on data analysis workshops several times a year, including a workshop series on spatial transcriptomics, as well as workshops on RNASeq and single cell RNASeq analysis. You can access recordings and materials from past workshops, along with other bioinformatics educational resources through the GRC’s Blackboard Course; passcode: GenomicsWorkshop.
2. University of Rochester’s Center for Integrated Research Computing (CIRC) offers workshops and bootcamps to build knowledge of the BlueHive computing environment and other computing resources supported by CIRC.
3. Office of Research IT has a series of resources to support research in the School of Medicine and Dentistry, including the next generation computing platform, Momentum.