Proteomics Training Program

The training program in Advanced Proteome Informatics of Cancer, funded by the National Cancer Institute, supports students performing graduate cancer-related research and provides training for proteome informatics research. The National Cancer Institute has made a substantial investment in new technology platforms for cancer proteomics, especially through the Mouse Models of Human Cancers and the Clinical Proteomic Technologies for Cancer and this investment is expected to result in greatly increased application of proteomics to cancer research.

The proteome is critical to understanding functional genomics and systems biology of cancers and to discovery and validation of biomarker candidates and molecular targets for therapy and prevention. Sophisticated analysis of proteomes requires advanced informatics to deal with the complexity of specimens, the extreme dynamic range of protein concentrations, post-translational modifications, alternative splice isoforms, responses to all sorts of perturbations, and differences in databases. The current scarcity of trained scientists in this subdiscipline of bioinformatics is the focus of this T32 training grant.

The PICTP builds on our successful experience with the Bioinformatics Graduate Program, based in the university-wide Center for Computational Medicine and Bioinformatics (CCMB). This program takes advantage of the robust community of cancer researchers, bioinformaticians, statisticians, chemists, and software engineers at the University of Michigan to focus on major challenges in proteome data analysis. Trainees come from diverse backgrounds and will receive training in cancer biology, bioinformatics, and computer science through courses, seminars, journal club, and annual retreats. The main goal of this training program is to provide a new pool of scientists well-equipped for independent careers in cancer research, contributing to NCI goals.

Student trainees will be expected to participate in all PICTP courses and other activities. Mentors will participate in PICTP activities as outlined in the attached program summary.

Nomination Process

A call for nominations will be sent to all affiliated faculty on an annual basis. Nominations of students outside of the Bioinformatics Program are welcome. Faculty sponsors who are not yet members of the PICTP should also submit a description of the research environment of their laboratory, including the mentoring plan. They should also indicate their willingness to participate in PICTP activities and apply to join PICTP faculty. For clarification of policies or of the application process, please contact: Alexey Nesvizhskii.

Program Requirements

Courses

Trainees are also expected to take courses in four of five key areas (Molecular Biology, Databases and Computing, Probability and Statistics, Biophysics and Structural Biology, and Systems Modeling and Analysis) in order to demonstrate reasonable competence in these fields. Students are encouraged to take courses offered by the Cancer Biology Program.

Student Responsibilities

In addition to participation in the core courses and program activities, trainees will fulfill the following: The thesis committee will include at least one PICTP core faculty member other than the thesis adviser, revise their research description on an annual basis, plus provide reporting information required by the funding agency. You must acknowledge the training grant in all publications referencing research while appointed. The information you need is this: Advanced Proteome Informatics of Cancer (T32 CA140044). Also, all publications should be submitted to PubMed Central in accordance with the NIH requirements.

Faculty Responsibilities

In addition to ensuring that the PICTP trainees fulfill their obligations to the PICTP program, faculty mentors are expected to participate in PICTP events, administration, and courses. Events include the Fall Kickoff for the Bioinformatics program, workshops, and recruitment events.