Research & Collaboration

The Gladstone Bioinformatics Core is actively involved in research collaborations. There may be opportunities for your group to collaborate on projects outlined in ongoing grants or grants in preparation. Let us know if you are interested in a potential collaboration!

  • We have CVs and FTEs to add bioinformatics and biostatistical expertise to your grant applications.
  • We have award-winning writing samples to adapt into your grants describing bioinformatics analysis and software development.
  • We have the capacity to hire, train and manage new personnel for any size bioinformatics project.
  • Scroll down for our publications section.

Collaboration

If your current research involves longer-term bioinformatics analyses and you are seeking personnel to complete these aims, we can provide partial FTEs or consultation for new hires. If your research aims synergize with our own grant-funded projects, then we might collaborate around a common goal. See current examples of our funded research projects.

New Grant Proposals
If you have a longer-term project in mind involving bioinformatics or data visualization and analysis, we can provide a standard description of the capabilities, expertise and relevance of the Gladstone Bioinformatics for your grant proposal. Depending on the topic and relevance to our own research goals, we could provide customized aims and even preliminary work. A major goal of our center is to support and promote Gladstone research. Specialized bioinformatics sections can give distinct advantage to a wide range of grant proposals.

Joint Publications
Where your research interests intersect with those of Gladstone Bioinformatics, we can pursue co-authored publications. For example, if you need a custom data visualization that contributes to our own development projects, we could collaborate around the analysis and presentation of your data. This could be an isolated data figure in a software development article. Or, it could be a brief software or method introduction in a basic research article

Our Ongoing Research Projects

The Gladstone Bioinformatics Core is actively involved in research and development projects. These are a few of our ongoing projects. Let us know if you would like to know more about our research or collaboration opportunities.

NRNB Software Development and Training
Members of the Gladstone Bioinformatics Core helped establish the new National Resource for Network Biology (NRNB), which is dedicated to development, distribution and support of network biology software and resources. We are developing new visualization methods for exon, probeset, SNP and protein domain level data. We are developing tools to transform massive "hairball" interaction networks into manageable pathways with biological context. And we are developing training infrastructure and materials to put these tools and resources in the hands of bench biologists.

NHLBI Bench to Bassinet
The Bench to Bassinet Program (B2B) is a major effort launched by the National Heart, Lung, and Blood Institute to learn more about how the heart develops and why children are born with heart problems. Cardiac development is a finely orchestrated process involving numerous genetic and epigenetic components. Developmental studies of cardiac function and disease employ diverse approaches, each of which sheds light on a different aspect of heart biology. The B2B consortium aims to bring these approaches together for an integrated, collaborative analysis of cardiac development. The B2B Bioinformatics Core, which is based at Gladstone, will help realize the great potential of this project by using and developing cutting-edge computational tools for translating raw data from diverse data types and different species into meaningful biological results.

GenMAPP-CS Development
Nearing completion, this 5 year software development project has resulted in a newly redesigned version of the popular pathway analysis tool, GenMAPP. Globally recognized as a unique and powerful analysis resource, GenMAPP development has lead to WikiPathways and now GenMAPP-CS.

WikiPathways Development and Pathway Curation
We recently submitted an R01 grant proposal to fund continued development and content curation for the WikiPathways project. The aims include a focused program of new pathway creations based on cutting edge research performed here at Gladstone and beyond. If your research involved biological pathways and you are interested in pathway representations amenable to data visualization and presentation, then let us know.

AltAnalyze - Alternative Splicing Analysis Software
AltAnalyze is a freely available, cross-platform application designed to assess changes in protein sequence, domain composition, and microRNA targeting from user RNA sequencing (RNASeq) or microarray data (Affymetrix Exon, Gene and Junction arrays). To do this, AltAnalyze associates user sequence-level changes in exon or junction expression that lead to the alternative expression of associated mRNAs. Basic methods for conventional microarray analysis are also available (RMA summarization, statistics, annotation and pathway over-representation).

Collaboration with PSI to Target and Interpret Protein Complexes that Regulate Transcription in ES Cells
The major goal of this proposal is to reveal molecular mechanisms underlying formation and function of critical transcriptional assemblies essential to embryonic stem cells and cells with induced pluripotency cells. We have identified a set of related genes to be considered as possible targets, starting from the list of already identified targets. We have also constructed a pathway at WikiPathways by augmenting a pluripotency-related pathway with targets and interaction information. Both the network visualizations from Cytoscape and the pathway diagram have been used in presentations and grant progress reports.

Bioinformatics Core Publications