Bioinformatician

The Experimental immunology laboratory and the Center for Omics Sciences (COSR) of the San Raffaele Scientific Institute in Milan, Italy, jointly seek a bioinformatician to join a recently funded ERA-NET TRANSCAN-3 international project. The main objective of the project is to define and validate in an international consortium predictive mechanisms of response to pre-surgical therapy in the esophageal adenocarcinoma.
The successful applicant will computationally investigate the molecular and immunological determinants of response to therapy in esophageal adenocarcinoma by analyzing data obtained by tumor whole exome sequencing, RNA sequencing and single-cell spatial transcriptomics, as well as T cell receptor sequencing of tumor-reactive T lymphocytes. Familiarity with command line interface, bash shell and at least one language between R and python are considered a necessary prerequisite for this position. Previous experience in NGS data analysis is an important prerequisite and the ability to deal with single cell transcriptomics will be considered a strong advantage.
The bioinformatician will be embedded in the COSR, which hosts several Illumina sequencing machines and one of the largest bioinformatic groups in Italy. COSR in involved in a large number projects, both within and outside the San Raffaele hospital, spanning clinical to basic research. It relies on an on-premise HPC cluster and is a very collaborative environment, where people can share expertise and pipelines. The San Raffaele Hospital is the largest biomedical institute in Italy offering highly integrated multidisciplinary approaches in which wet, dry and clinical science closely cooperate to both identify disease mechanism and explore ways to harness them for therapeutic benefits.

Key Recent Publications from the Hosting Lab
Mennonna, D., Maccalli, C., Romano, M. C., Garavaglia, C., Capocefalo, F., Bordoni, R., Severgnini, M., de Bellis, G., Sidney, J.,Sette, A., Gori, A., Longhi, R., Braga, M., Ghirardelli, L., Baldari, L., Orsenigo, E., Albarello, L., Zino, E., Fleischhauer, K., Mazzola G, Ferrero N, Amoroso A, Casorati G, Parmiani G,Dellabona, P. (2017). T cell neoepitope discovery in colorectal cancer by high throughput profiling of somatic mutations in expressed genes. Gut, 66(3), 454-463.
Arbore, G., Albarello, L., Bucci, G., Punta, M., Cossu, A., Fanti, L., Maurizio, A., Di Mauro, M., Bilello, V., Arrigoni, G., Bonfiglio, S., Biancolini, D., Elmore, U., Puccetti, F., Vago, L., Cascinu, S., Tonon, G., Rosati, R., Casorati, G., Dellabona, P. Pre-existing immunity drives the response to neoadjuvant chemotherapy in esophageal adenocarcinoma. Cancer Research 2023, in press

**Main activities**:
Analysis of NGS datasets.

**Who we are looking for**:
An enthousiastic scientist with coding experience.

**Work details**:
**Type of contract**: cococo;
**Place of work**: IRCCS San Raffaele Hospital, Milan, Italy.