Bioinformatics Core

Bioinformatics Core

Bruce Aronow, PhD, Co-director, Computational Medicine Center, Professor, University of Cincinnati, Department of Pediatrics. Email: bruce.aronow@cchmc.org

Winston Hide, PhD, Associate Professor of Bioinformatics and Computational Biology, Scientific Director, Bioinformatics Core Harvard School of Public Health. Email: whide@hsph.harvard.edu

Alexander Pico, PhD, Associate Director of Bioinformatics at the Gladstone Institutes and Executive Director for the National Resource for Network Biology. Email: apico@gladstone.ucsf.edu

Nathan Salomonis, PhD, Assistant Professor, University of Cincinnati Department of Pediatrics at Cincinnati Children’s Hospital. Email: nathan.salomonis@cchmc.org

Lynn Schriml, PhD, Associate Professor, University of Maryland, School of Medicine in the Department of Epidemiology and Public Health and at the Institute of Genome Science (IGS) in Baltimore, Maryland.   Email: lschriml@som.umaryland.edu

Objective:

The bioinformatics core aims to provide investigators within the PCBC access to genomics analysis tools, automated analysis pipelines, fully analyzed sequencing datasets and raw data for distinct iPS technologies and cell types (pluripotent and differentiated products). Our initial goal is to generate a cross-connectivity map across multiple omics data-types to reveal pluripotency differentiation pathways and intuitive navigations tools for these data (Synapse, ToppGene). Core members are available to help integrate this data into the analyses of PCBC investigators as well as support for associated analysis tools. We are further working on automated pipelines to analyze both PCBC omics datasets or PCBC investigator datasets in a fully automated manner from array/sequence directly to web navigatable graphs and spreadsheets.

Associated Resources:

• Sage Synapse [https://www.synapse.org/#!Synapse:syn1773109] (contact: larsson.omberg@sagebase.org)
  • (account set up for Snyapse: /content/synapse)
• ToppGene [http://toppgene.cchmc.org/] (contact: bruce.aronow@cchmc.org)
• AltAnalyze [http://www.altanalyze.org] (contact: nathan.salomonis@cchmc.org)
• PathPrints [http://compbio.sph.harvard.edu/hidelab/pathprint](contact: shosui@hsph.harvard.edu)
• Cytoscape [http://www.cytoscape.org] (contact apico@gladstone.ucsf.edu)

For assistance in the use of bioinformatics core resources, posted analyses or possible collaborations of interest in your hub site please contact specific core investigator.