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The NIH T32 Research Training Program in Gastrointestinal Surgery will be focused on providing trainees with the tools necessary to genuinely bridge the gap between laboratory observations and applied diagnostics and therapeutics. Residents will devote a minimum of two years with a possible extension to three years to full-time research in their mentor’s laboratory. The training program blends a combination of mentored research training and didactic training, as discussed below. Residents will receive rigorous training in the general scientific method, including critical review of the literature, development of a hypothesis or identification of an unmet clinical need, experimental design and execution, data analysis and interpretation, scientific writing and oral presentation. The Executive Committee and the Research Committee will meet biannually to evaluate the trainee's progress.

Research Tracks

In addition to a Base Curriculum applicable to all trainees, each trainee will elect a specific program tailored to  the development of sophisticated skills in one of three research tracks: 

Preclinical Research Track

Those engaged in the Preclinical Research Track will work on a laboratory-based project focused on a disease process. In addition, those trainees will select amongst an array of didactic courses and workshops designed  to promote their development into independent investigators.

Clinical Research Track

Similarly, trainees in the Clinical Research Track will be mentored through their participation in an active clinical research study, bolstered by their choice of additional coursework in clinical trial design, biostatistics and/or epidemiology.

Translational Research Track 

The Translational Research Track highlights opportunities unique in their breadth and depth to UCSF, the Bay Area and Silicon Valley. These trainees can access resources and educational experiences spanning the gamut of product development, commercialization and bio-entrepreneurship, including courses on intellectual property and financing startups, weekly workshops on bioentrepreneurship, and participation in business plan competitions, in addition to the trainee’s work on a product in the premarket approval stage of development. The Executive Committee and Department of Surgery Research Committee, led by Peter G. Stock, M.D., Ph.D., will meet regularly, and at least biannually, to evaluate each trainee’s progress.

Mentorship and Training

Selection of a specific laboratory and mentor is a collaborative process beginning with the trainee based on their interests, relevant research background and career goals. Importantly, the Department of Surgery does not arbitrarily assign residents to laboratories.  Each trainee is teamed with a faculty member who will serve as their mentor and the principal investigator of the laboratory. Considering the quality and productivity of the faculty mentors, the trainees are guaranteed to work in laboratories with strong track records of success in research focused on important clinical problems relevant to diseases of the gastrointestinal tract. Workspace is located within the faculty mentors’ research laboratories where trainees work alongside postdoctoral fellows, research assistants and young scientists, thereby promoting the intellectual and practical cross-fertilization of ideas, techniques, and strategies. The training program blends a combination of mentored research training and didactic training, as discussed below. 

Preparation of the Proposal

Each applicant is expected to meet with his or her Core Faculty member 15 months before the anticipated start date of the training program, to develop a research program. Applicants  are required to write a 2 to 3 page research proposal that includes a brief literature review, a statement of the general research question and hypothesis, and a list of specific aims. The Department of Surgery Research Committee and the training grant’s Executive Committee independently review these proposals. The constructive criticism of the proposals from both reviewing bodies is considered an essential first step in the training program. However, only final approval of the research proposal by the Executive Committee is mandatory for each program participant. 

Base Curriculum

These courses are required for all trainees.

Introduction to Research Fundamentals (24 hours)

Recognizing that many trainees have little or no experience in research, the Department of Surgery has organized an immersion course in research. This 5- day course is held during the first week of July when the applicants begin their research fellowship, and is designed to jump-start the process by which the trainees starting thinking and communicating like clinician- scientists. The course includes the following topics, taught principally by the faculty mentors, along with a few guest lecturers.

Basic Introduction to Research

Michael A. Matthay, M.D., Department of Medicine
Hobart W. Harris, M.D., M.P.H., Department of Surgery

Topics will include basic research principles, publications, grants, ethics, regulatory requirements, experimentation with animals, and record keeping.

Detection of Proteins and Nucleic Acids

Valerie M. Weaver, Ph.D., Department of Surgery

Topics include gel electrophoresis, Western blotting, immunoprecipitation, Northern, Southern blotting, RT-PCR, genomic approaches, proteomic approaches, metabolomic approaches. Of note, this course is designed to familiarize trainees with common techniques and terminology so that they can better understand the literature and communicate with collaborators.

Working with Animals

Jacquelyn J. Maher, M.D., Department of Medicine
Michael Rosenblum, M.D., Ph.D., Department of Dermatology

Topics include proper animal model selection, humane treatment, expressing transgenes, gene knockout and silencing, cell and tissue specific genetic manipulation, breeding and colony management.

Introduction to Bioengineering & Device Development

Shuvo Roy, Ph.D., Departments of Bioengineering & Therapeutic Sciences and Surgery

Topics will include an overview of basic bioengineering approaches to life sciences research, mathematical modeling, design and prototypes. 

Scientific Writing Course (20 hours) 

Pamela Derish, M.A., Manager, Department of Surgery Publications Office  

While residents are in training, the Department of Surgery's Publications Office provides support for producing a body of research publications that will increase their eligibility for job placement and advancement as academic surgeons by offering an intensive formal course in scientific writing.  Since the ability to obtain extramural funding is critical to the success of young academic surgeons and scientists, and because grant writing requires a skillful blend of technical and non-technical writing that is targeted to a specific audience, the writing course devotes two weeks to proposal writing skills.  The writing course is offered twice a year (Fall and Spring) and is held over 8 consecutive weeks from 4 to 6 PM.  The course objective is for participants to learn specific ways to marshal the details of a biomedical research paper or grant proposal into a clear, concise and comprehensible story that will be understandable to an interdisciplinary readership (papers), or meet the agency’s review criteria (proposals).  

By carefully deconstructing published examples and their own writing, participants learn how precise word choice can eliminate jargon and ambiguities, how simple, direct sentences can describe complex science, and how organizing and developing ideas into paragraph form makes scientific writing logical and persuasive.  Participants will also learn that although they may think they have described a concept, experiment, or result in an early draft, careful reading will typically reveal information gaps, unrecognized assumptions, and faulty reasoning.  All of these problems can be fixed if the writer learns how to spot them, and how to revise them. The format of the course is as follows.

  • Part 1: Writing fundamentals (word choice, sentence structure, and paragraph structure) (2 weeks).
  • Part 2: Reports of original research (Introduction, Materials & Methods, Results, Discussion, Tables & Figures, Abstract and Title) (4 weeks; other types of papers, e.g., review articles and case reports/ case series, are covered in online presentations designed by the instructor).
  • Part 3: Publication ethics and the peer review process (1 week)
  • Part 4: Grant proposals (guest panelist: NIH-funded surgeon-scientist discusses the proposal writing and review process; developing hypotheses and aims; developing the Background, Significance, Preliminary Studies, and Methods sections (and for NIH grants specifically, the Approach section); Abstract and Title) (2 weeks).

The course combines didactic presentations with rewriting examples of unclear writing in class and outside of class.  Weekly homework assignments include revising or rewriting parts of a manuscript written by the participant. Participants receive detailed feedback on their writing from the course instructor.

Editorial Support Services

The Department's Scientific Publications Office also provides trainees with editorial support that enables them to maximize their research productivity, publications, and grant  applications. The Department’s editor and writing instructor is available to work closely with authors to prepare, produce, and submit documents that are of high quality with regard to organization and structure, accuracy and completeness, use of language, adherence to style and format requirements, and appearance. Grant  proposals and full-length articles, brief observations, review papers, case studies, editorials, letters, revisions, and cover letters for revisions can be submitted for editorial review.

The Art of Giving Scientific Talks (8 hours)

Hobart W. Harris, M.D., M.P.H., Department of Surgery
Pamela Derish, M.A., Department of Surgery
Michael A. Matthay, M.D., Department of Medicine

This course was designed in consultation with Mimi  Zeiger, who taught the highly regarded “Art of Lecturing and Slide Presentation Course” at UCSF for many years before retiring in June 2012. The course goal is to help residents improve their oral presentation skills for giving talks at national and international meetings. Participants learn both by giving their own talks and by critiquing others' talks. The four-week course meets for two hours weekly and is held once each year on the Parnassus Campus, in the Fall. Participants must already have a 15 or 20-minute talk they’ve prepared that they wish to improve on and 1-2 sample slides to submit before the first class meeting. The course format is as follows.

Week 1: Demonstration talk, instruction on preparing talks, giving clear talks, and illustrating talks.

Weeks 2-4: Talks by class members, followed by class discussion of the strengths of the talk and suggestions for improvement. Two people will present in week 2 and two in week 3. In week 4, all four participants will present a revised version of their talk.

Biostatistical Methods for Clinical Research (BIOSTAT 200) (36 hours)

Judith Hahn, Ph.D., M.A., Course Director
Department of Medicine

The course is an introduction to the study of biostatistics covering types of data, their summarization, exploration and explanation. Also, the trainees will look at concepts of probability and their role in explaining uncertainty, and end with coverage of inference applied to means, proportions, regression coefficients and contingency tables. Throughout the 13-week course, the trainees will attend a combination of lectures and computer labs wherein the software program STATA will be used. 

Clinical Research Workshop (20 hours)

This seven-week workshop includes four courses that are the starting point for all clinical research training at UCSF. These courses introduce the field of clinical research by providing instruction in the design of clinical research studies, collecting and managing clinical research data, and preparing for a career in clinical research. For individuals who will participate in clinical research in a supportive capacity, the Workshop alone is sufficient training. For others desiring to be independent investigators, the Workshop serves as introductory material for the more advanced ATCR Certificate and Master's Degree in Clinical Research Program. 

Specialized Training 

These courses are “electives” offered to enable the trainees to develop the specialized skill sets and expertise appropriate for their specific area of research focus and long-term career goals. The choice of additional didactic coursework will be individualized with each trainee working in close concert with their faculty mentor and the Executive Committee to design a course of specialized training that is specifically tailored. 

The curriculum will be designed taking into account the background, special interests and overall professional goals of the trainee so as to optimize their experience, productivity and chances for future success as an innovative, independent clinician-scientist. Accordingly, UCSF offers a broad range of course options relevant to three research tracks, including some certificate and master’s degree programs. Trainees will be expected to receive 60-100 hours of didactic instruction within their specific focus area during the second year of the fellowship. What follows are examples, not an exhaustive list of available electives. 

Preclinical Research Track

Semester-long graduate level courses that generally consist of lectures or small group discussion groups for 4 hours a week for 3 months plus additional reading assignments, e.g.,

  • Molecular and Cellular Immunology
  • Structural Biology & Biophysics
  • Signaling Mechanisms 

Clinical Research Track

  • Designing Clinical Research (1 month)
  • Advanced Training In Clinical Research Certificate Program (1 year)
  • Master’s in Clinical Research (2 years; candidates interested in this program will be identified prior to starting the fellowship) 

Translational Research Track

  • Modern Methods in Drug Discovery (5 weeks)
  • Idea to IPO (course in bioentrepreneurship, 12 weeks)
  • Translational Challenges: Diagnostics, Devices &Therapeutics (12 weeks)
  • Master’s in Translational Medicine (1 year) 

Training Program Milestones 

At the conclusion of the two-year fellowship, the goal is for each trainee to have participated in a series of prescribed and elective didactic courses, made research presentations at local and national meetings, and written at least two abstracts, two original manuscripts and a grant application based on their work. The overarching goal is for the trainees to have a rich, robust and productive research fellowship that provides them with the tools for future professional success and enhances their value as prospective junior faculty hires. The anticipated timeline for these program milestones are outlined in the table A  below.


Year 1

Year 2


Didactic Coursework (classroom hours)




Conference Presentations




Abstract Submissions




Department of Surgery Resident Research Program Presentations




National Meeting/Conferences




Original Manuscript Submissions




Grant application




Table A - Training Program Milestones Timeline

Research Conferences

Each trainee is required to attend a monthly Training in Gastrointestinal Surgery Research Conference and present their work-in-progress at least twice each year. The monthly conferences will typically include presentations by trainees and/or established investigators engaged in preclinical, clinical and/or translational research, thereby ensuring regular interaction and collaboration across these disciplines. Trainees will receive formal coaching in advance of the presentation and formal feedback at the end of the presentation. Members of the training program’s faculty will attend the Training in Gastrointestinal Surgery Research Conferences and are thus well positioned to provide feedback regarding the relative strengths/weaknesses of the presentations. In addition, trainees are encouraged to choose from the rich selection of regular research conferences throughout the UCSF campuses, including numerous journal clubs, which are well attended by trainees from across departments.

Trainee Evaluation

The Research Committee of the Department of Surgery and the T32 Training Executive Committee will evaluate the trainees, their laboratory mentors and the didactic components of the training program.

The Research Committee, chaired by Dr. Peter G. Stock, will actively participate in overseeing the trainees and their laboratory mentors. The Research Committee collaborates with the Executive Committee in overseeing the research training of program participants, including UCSF general surgery residents, and those from the UCSF East Bay Surgery Program and other institutions who were elected to do their research training within the UCSF Department of Surgery.


The Executive Committee will meet twice a year (Fall and Spring quarters) to evaluate the trainees and their mentors. All trainees and their mentors will be invited to the Fall meeting, which will be held in conjunction with the Research Committee, and where the residents will deliver a 30-minute presentation about their research, followed by 15 minutes of general discussion and feedback. Residents will be able to present the background and plans of their project (if they have recently started their research training) or will summarize their progress.

  • The Research Committee meets with all residents during their first and second years of residency to inform them of the training opportunities at UCSF. Individual residents are then assigned to committee members for one-on-one advice and counseling. The intent is to match residents with training opportunities that are optimal for their chosen career path.
  • Fifteen months before residents commence research training, the Research Committee requires that residents and their mentors submit a research proposal. Candidates suitable for the Training in Gastrointestinal Surgery Program will be paired with a Core Faculty member who will be actively participating in the process of defining the appropriate research track. The 2 to 3 page research proposal includes the background and significance of the project, a statement of the research question and hypothesis, and the specific aims. The Research Committee provides constructive criticism to the trainees and their mentors. In addition, each trainee will begin work on an Individual Development Plan (IDP). The IDP will be a dynamic and evolving mentoring plan that begins with a thoughtful and thorough analysis of the trainee’s background and interests, followed by identification of the trainee’s specific needs vis-à-vis their short- and long-term career objectives.
  • For the remainder of the trainees’ research experience, the Research Committee serves as an adjunctive review body, providing additional objective analysis of the trainees’ progress in addition to that provided by the Executive Committee. We feel that a multifaceted, unbiased evaluation of the trainees and the training program is essential to developing and maintaining the best possible training program.
  • After 3 months of research training, the Research Committee meets with the trainees to hear an update about the planned research and to review the trainee’s IDP. The Research Committee wishes to know whether the trainees have a well-developed and suitably focused project, and to ensure that they are well integrated and suitably supported in their chosen research groups.
  • After  12 months of research training, the Research Committee meets with the trainees and their mentors to ensure that the trainees are making satisfactory progress and to refine their IDP, as indicated. The Committee expects an update of the work accomplished, a summary of the plans for the following year, and information about any difficulties or unanticipated problems. This annual review by the Research Committee coincides with the biannual (Fall and Spring quarters) review conducted by the Executive Committee. The Fall review will include a research presentation by each trainee and will be conducted in concert with the Research Committee.
  • Within 1 month of completing the training, each trainee is required to submit a written report summarizing their accomplishments, presentations, publications and awards to the Executive Committee and the Research Committee. Furthermore, the trainees are required to provide to both Committees confidential evaluations of their mentors. Similarly, the mentors evaluate their trainees. All trainees are expected to present their work at the annual Residents Research Day (which is open to the entire University) during each year of the fellowship. Importantly, written feedback will be provided to the trainees and their mentors about their research plans and progress jointly from the Executive and Research Committees.
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