For larger projects BICF staff can be engaged through investigator-funded contributions of an appropriate FTE level for a defined project duration. The goal of this service is to provide researchers access to highly qualified bioinformaticians, without the challenges of recruiting and retaining personnel in their labs. During a project, staff members are typically “embedded” part-time with a client lab, while remaining housed with and with the supervision of the BICF.
Since its formation, the BICF has engaged in over two dozen collaboration projects. All scripts, including those to generate figures in papers, are managed in a source control repository. Codes are made publicly available before or concurrent with the submission of manuscripts, to ensure reproducibility and provenance. In many of these projects, the level of BICF staff involvement usually warrants authorship, although the decision remains the hiring PI (see Authorship, Acknowledgement and Software).
Following are three recent example publications arising from this program (see also Publications; BICF staff in bold):
- Zhang Z, Zhou C, Li X, Barnes S, Hoover E, Chen C, Metang L, Navrazhina K, Deng S, Cao Z, Wongvipat J, Choi D, Johnson N, Huang C, Wang C, Lee YS, Lee E, Yun D, Linton E, Chen X, Liang Y, de Stanchina E, Abida W, Lujambio A, Li S, Lowe S, Malladi V, Sawyers L, Mu P. Chromatin changes precipitated by CHD1 loss result in heterogeneous mechanisms of hormone therapy resistance in prostate cancer. Cancer Cell (2020), https://doi.org/10.1016/j.ccell.2020.03.001, in press.
- Hassounah NB*, Malladi V*, Huang Y, Freeman SS, Beauchamp EM, Koyama S, Souders N, Martin S, Dranoff G, Wong KK, Pedamallu CS, Hammerman PS, Akbay EA. Identification and characterization of an alternative cancer-derived PD-L1 splice variant. Cancer Immunol Immunother. 2019 Mar;68(3):407-420.
- Li S, Chen K, Zhang Y, Barnes S, Jaichander P, Zheng Y, Hassan M, Malladi V, Skapek SX, Xu L, Bassel-Duby R, Olson EN, Liu N. Twist2 amplification in rhabdomyosarcoma represses myogenesis and promotes oncogenesis by redirecting MyoD DNA binding. Genes Dev. 2019. 33:626-640.