© 2007

Freund/OncoLab

The group

bio))flag is a genomics-based discovery company focused on the identification and development of novel biomarkers through the application of bioinformatics, biology, chemistry, and medicine. The growing interest of patients, doctors, insurance providers, and policy makers towards personalized medicine makes biomarkers an attractive market for the biopharmaceutical industry since they can define a disease more accurately than conventional diagnosis. The development of therapeutics based on biomarkers can treat the disease more selectively and safely and have a better defined mechanism of action for more predictable response, as well as increasing the success rate of clinical trials for new drugs due to a more accurate patient selection. Biamarker-based therapy development improves the cost-effectiveness of pharmaceutical development and testing, and should reduced adverse effects of therapy. bio))flag is located in the Science Park of Sardinia (Cagliari, Italy), and stems from the founder scientists’ research in the fields of gene expression, molecular oncology and bioinformatics. The outcome of this unique competence is the development of integrated biological, experiment-based and in silico-based technology platforms that permits the identification, selection, prioritization and validation of novel targets. Our company strategy is pursuing our own internal discovery process and exploiting proprietary research and technologies to generate a consistent IP portfolio and develop pre-clinical and early clinical evidence for promising biomarkers, whose use and development can subsequently be negotiated with major biopharmaceutical companies.

Our role in EET-Pipeline

Using a combination of bioinformatics, molecular biology and pathology, bio))flag will identify novel biomarkers for embryonal tumor types. In particular, a validated collection of antisense transcripts, antigens and antibodies associated to embryonl tumors will be generated. To achieve this goal, bio))flag will apply bioinformatic tools in combination with a supercomputing capacity to mine the gene expression databases available from public institutions as well as data generated by the E.E.T-Pipeline consortium partners to identify highly enriched non-coding RNAs (in particular, natural anti-sense transcripts) and novel tumor-specific surface proteins. The main selection for candidate molecules will be pursued via analysis of the transcriptome, which represents the computational framework where a dedicated discovery search engine identifies the over-represented expressed sequences that are either rare/polymorphic transcripts, splice variants, or non-coding transcripts, all of which are associated with the specific cellular and molecular profile of the tumor. Once candidate sequences are selected and internally validated, the pipeline involves a direct high-throughput production of the predicted most antigenic regions of the corresponding proteins. These are then used for the production of mouse polyclonal antibodies and immunoassay panels, to directly assess their distributions and amounts in tumor and body fluid samples as compared with normal non-affected patient materials.

Staff Member

Top 5 publications

1. Quinn JC, Molinek M, Martynoga BS, Zaki PA, Faedo A, Bulfone A, Hevner RF, West JD, Price DJ. Pax6 controls cerebral cortical cell number by regulating exit from the cell cycle and specifies cortical cell identity by a cell autonomous mechanism. Dev Biol. 2007 Feb 1;302(1):50-65.

2. Bulfone A, Carotenuto P, Faedo A, Aglio V, Garzia L, Bello AM, Basile A, Andre A, Cocchia M, Guardiola O, Ballabio A, Rubenstein JL, Zollo M. Telencephalic embryonic subtractive sequences: a unique collection of neurodevelopmental genes. J Neurosci. 2005 Aug 17;25(33):7586-600.

3. Lavorgna G, Triunfo R, Santoni F, Orfanelli U, Noci S, Bulfone A, Zanetti G, Casari G. AntiHunter 2.0: increased speed and sensitivity in searching BLAST output for EST antisense transcripts. Nucleic Acids Res. 2005 Jul 1;33

4. Englund C, Fink A, Lau C, Pham D, Daza RA, Bulfone A, Kowalczyk T, Hevner RF. Pax6, Tbr2, and Tbr1 are expressed sequentially by radial glia, intermediate progenitor cells, and postmitotic neurons in developing neocortex. J Neurosci. 2005 Jan 5;25(1):247-51.

5. Faedo A, Quinn JC, Stoney P, Long JE, Dye C, Zollo M, Rubenstein JL, Price DJ, Bulfone A. Identification and characterization of a novel transcript down-regulated in Dlx1/Dlx2 and up-regulated in Pax6 mutant telencephalon. Dev Dyn. 2004 Nov;231(3):614-20.