Biomedical Informatics Scientific Collaborations

The elucidation of oncogenetic and tumor progression processes often requires the development of novel methodologies or the creation of complex clinical and bioinformatic work-flows that may be beyond the expertise of a well-trained bioinformatics service specialist. This is especially the case with the emergence of new cancer systems biology approaches that use fine-grain pathways and molecular interaction models to help identify dysregulated processes and causal lesions. As a result, a key function of the BISR is to build partnerships between HICCC members and investigators of DBMI, C2B2, and MAGNet. Currently, the BISR has collaborated on over a half dozen successful projects between computational and experimental scientists have been created thanks to the BISR. Some (Wang, Dalla Favera, etc.) have resulted in publications and in successful or pending cancer related grant applications.

Furthermore, several of these collaborations have resulted in new tools and methodologies that have since been integrated in the BISR toolkit of software and databases. Some clear examples of the tools that have emerged from these collaborations and are now integrated in the BISR toolkit are:

1. the geWorkbench platform for integrated genomics analysis (Califano/Floratos).

2. Several algorithms for cellular network reverse engineering including:

1. ARACNe and, MINDy (Califano)

2. MEDUSA extension from yeast to human cells (Leslie and Wiggins)

3. REDUCE extension from yeast to human cells (Bussemaker)

3. the GeneWays algorithm for the analysis of literature data (Rzhetsky)

4. the Cellular Network Knowledge Base (CNKB) which currently include human B lymphocyte interactions and is being extended to include similar interactomes for normal and tumor related breast, prostate, bladder, and T cell tissue (Dalla Favera, Ferrando, Cordon-Cardo, Califano).

5. A variety of tools for the integrated analysis of transcription factor data, including gene expression profiles, ChIP on chip, promoter sequences, and full gene phylogeny data (Ferrando, Dalla Favera, Califano, Bussemaker).

6. A workflow for the analysis of cDNA libraries for the identification of novel, tissue specific micro RNAs (Dalla Favera, Califano).

These tools, while developed and published in the context of an individual collaboration, are being made available to the entire HICCC community via the MAGNet dissemination process. The BISR support staff is available to either use these tools on demand, based on a specific research project request, or to train lab personnel in their utilization, or to integrate them in more complex research workflows.