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Bioinformatics

Biological informatics (bioinformatics) concerns the analysis and interpretation of various types of data including nucleotide and amino acid sequences, protein domains, and protein structures. Informatics helps us to understand and organize different types of information, and to see patterns in the information. The Bioinformatics Core aims to provide expert consultation by developing informatics strategy for analysis of complex data sets for RI-INBRE-supported investigators, and educate faculty and students regarding bioinformatics approaches for their research in the RI-INBRE thematic areas.  The Bioinformatics Core works closely with the INBRE Centralized Research Core Facility and the Genomics and Sequencing Center at URI to coordinate analyses that require multiple computational and experimental resources.  We also maintain contact with other cores and user facilities in Rhode Island and New England and can refer you if your research needs can’t be met with available resources.

If you utilize the core services, please remember to acknowledge the core facility in your future correspondence.  For small-scale analyses, a line in the Acknowledgements sections of your manuscript is sufficient.  For larger-scale analyses, please consider including core personnel as co-authors.  Also be sure to keep us informed of any manuscripts or grant submissions involving the core so that we may keep metrics for reporting to NIH.


Bioinformatics Consultation and Services

We offer a variety of services to users, from consultation on bioinformatics problems to full research collaborations.  Resources currently available or that will soon be available include:

  • Genome assembly and annotation
  • Gene expression analysis (RNA-Seq)
  • Chromatin immunoprecipitation analysis (ChIP-Seq)
  • Molecular modeling (homology modeling, etc.)

Other resources may be made available upon request.  We maintain a Linux server at URI for analysis by core staff or by individual researchers if they would like to run analyses themselves.

Bioinformatics Resources

The scope of bioinformatics resources available to researchers is vast and growing.  Here we provide links to common resources likely to be useful to INBRE researchers.  Core personnel are available to assist individual researchers with using these tools and dedicated workshops will be periodically provided as part of the Core’s educational outreach mission.

Workshops and Tutorials

The Bioinformatics Core will periodically offer workshops covering specific bioinformatics skills including sequence analysis, molecular modeling and scientific programming.  This section will contain information for upcoming workshops, information about past workshops and useful online tutorials/lectures.  We are planning a series of workshops this summer on Introductory R for Statistical Analysis and will likely include workshops on gene expression analysis and other scientific topics in the future.  We also offer traveling workshops to the RI-INBRE institutions to cut down on your travel time.  If there are specific topics you would like to see covered, please contact us.  Please watch this space or subscribe to our listserv (see below) to keep up to date on workshop availability.

Personalized Training

In addition to our workshops and tutorials, we also offer personalized training to students and faculty in basic bioinformatics techniques just as basic data mining, genome assembly and annotation, BLAST, multisequence alignment, phylogenetics, and other topics.

INBRE Seminar Speakers

Each semester, INBRE sponsors 4-5 external speakers as part of the Biomedical and Pharmaceutical Sciences Department seminar series.  If you have suggestions for seminar speakers, particularly in the areas of molecular toxicology/natural products, cancer biology, and neurosciences, please contact us.

Citing the Bioinformatics Core

If you use the core services, we ask that you include the following acknowledgement in any manuscripts or presentations involving your research: “This research is based in part upon work conducted using the Rhode Island IDeA Network for Excellence in Biomedical Research Bioinformatics Core which is supported by the National Institutes of Health under grant 2P20GM103430”.  For more extensive collaborations, we will also request co-authorship on any manuscripts resulting from the work.  If you have a proposal idea that requires a bioinformatics component, please contact us to discuss a formal collaboration.

Bioinformatics Listserv

To simplify communication and keep our users up to date on Core functions, we have set up a listserv at URI.  To join the listserv, send an email to listserv@listserv.uri.edu with the following in the body of the message: subscribe INBRE-BIOINFO your name

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