Home Education BIT Program Overview Predoctoral Program

Predoctoral Program

Admission Procedures

Recruitment of first-year students directly into the BIT Program through the MCB OR MCP Gateway Programs will be performed in a manner similar to recruitment of first-year students into other campus graduate programs.

Program Clip Image

The Biomedical Informatics Training (BIT) Program. EG, Evolutionary Genetics track in Ecology & Evolutionary Biology Dept.; CMB, Combined Cellular & Molecular Biosciences Program in the School of Biological Sciences and the School of Medicine; MSTP, Medical Scientist Training Program; CB, Chemical Biology track in Chemistry Dept.; ChaMP, Chemical and Material Physics Program; BICB, Biomedical Informatics and Computational Biology track in Computer Science Dept; BME, Biomedical Engineering Program. While the BIT Program normally admits student at the beginning of their second year, BIT also recruits and admits students through two first-year gateway programs, the Mathematical and Computational Biology (MCB) Gateway Program and the Medicinal Chemistry and Pharmacology (MCP) Gateway Program.

Nomination Process

Applications for acceptance into the BIT Program will be received directly from first-year applicants. Applications accepted for admission by the BIT Steering Committee will be secondarily evaluated by the admissions committee of the campus graduate program in which they will receive their Ph.D. degree. Only applicants qualified for both programs can be accepted into the BIT Program. Criteria for acceptance in both programs is based on the student’s undergraduate and graduate academic and research record, GRE scores, and reference letters. Students with superior research experience, academic records, and GRE scores above the 75th percentiles will qualify for acceptance. Upon acceptance into the BIT Program, first-year students will be assigned a BIT faculty advisor in their primary area of interest. At the end of the first year of study, those students who successfully fulfill training program requirements and pass their program qualifying examinations, will select a BIT Program thesis advisor. As soon as possible, no later than the beginning of the winter quarter of the second year, the students together with the consultation of the BIT Program Steering Committee and their thesis advisor will select a cross-discipline co-thesis advisor. In most cases, this will be an investigator with ongoing collaborations with the student’s thesis advisor in areas related to the student’s thesis research.

As in the past, nominations for appointment of second-year graduate students to the BIT Program will be received from a student’s BIT Program faculty thesis advisor in an existing campus graduate program. These applicants will be evaluated by the BIT Program Steering Committee using the same criteria used for the admission of first-year students. In addition, their first year performance in UCI graduate courses and research rotations will be considered. Upon acceptance into the BIT Program, a cross-discipline thesis co-advisor will be assigned to each student. In most cases, this will be an investigator with ongoing collaborations with the student’s thesis advisor in areas related to the student’s thesis research.

Mandatory Courses

By the end of the first quarter of the second year, all students - whether they enter the BIT Program in their first year through the Gateway or in their second year though a BIT-affiliated graduate program - must have satisfactorily completed a high level language programming course equivalent to I&C Sci 21. The I&C Sci 21 course provides students with an introduction to fundamental concepts related to computer software design and construction, and design and programming skills, primarily using PERL and C++/Java/Python, emphasizing biological data and applications.

By the end of the second year of the BIT Program, all BIT students must pass the following four required BIT Program courses:

CS 284A. Representations & Algorithms for Molecular Biology (4) Fall quarter- Introduction to computational methods in molecular biology, aimed at those interested in learning about this interdisciplinary area. Covers computational approaches to understanding and predicting the structure, function, interactions, and evolution of DNA, RNA, proteins, and related molecules and processes. Prerequisite: a basic course in algorithms, or a basic course in molecular biology, or consent of instructor.

CS 284B. Probabilistic Modeling of Biological Data (4) Spring quarter- A unified Bayesian probabilistic framework for modeling and mining biological data. Applications range from sequence (DNA, RNA, proteins) to gene expression data. Graphical models, Markov models, stochastic grammars, structure prediction, gene finding, evolution, DNA arrays, single- and multiple-gene analysis.

CS 284C. Computational Systems Biology (4) Spring quarter- Computational inference and modeling of gene regulation networks, signal transduction pathways, and the effects of regulatory networks in cellular processes, development, and disease. Introduction of required mathematical, computational, and data handling tools.

MMG 250. Responsible Conduct of Research (2) Spring quarter- Every BIT Program student and postdoctoral fellow is required to take the UCI Responsible Conduct of Research course, no later than the end of the third year. This course, MMG 250 (2 credits), is offered each year during the spring term. All students on NIH training grants are required to participate in this course once during their training at UCI. The intent of this course is to introduce students to the complex issues involving scientific integrity, while meeting the requirements for training in bioethics for students supported on NIH training grants. The format for the course is informal and designed to engage students in discussion.

By the end of the third year of the BIT Program, all students must pass the following additional courses:

EE 240. Quantitative Methods in Biology (4) Winter quarter- Statistics for biologists, ecologists and evolutionary biologists. Emphasis on specific applications and underlying assumptions rather than on methods of calculation. Topics include experimental design, parametric and nonparametric methods, analysis of variance and covariance, and multiple regression.

CS 122A. Intro to Data Management (4) Winter & Spring quarter- Introduction to the design of databases and the use of database management systems (DBMS) for applications. Topics include entity-relationship modeling for design, relational data model, relational algebra, relational design theory, and Structured Query Language (SQL) programming.

CS 290. Elements of Scientific Writing (1) Fall quarter- New hands on course, started in Fall 2010, to teach graduate students how to write scientific papers, grant applications, and similar documents.

Most of the BIT-affiliated graduate programs require their students to take one elective course each academic year. The BIT courses described above will fulfill this requirement.

Click here for course requirements for BIT trainees who entered the program before AY06-07.

New Elective BIT Courses

Medical Informatics Course - New introductory course under development to be offered in Spring 2012 as a CS 295 to cover basic topics in Medical Informatics ranging from electronic medical records to personalized medicine.

High-Througput Sequencing Technologies and Applications - New course under development to be offered in Spring 2012 covering various high-throughput sequencing technologies and their applications to study gene expression (RNA-seq), regulation of gene expression (ChIP-seq), and genome sequence and variation, together with the corresponding data analysis tools and methods for downstream biological and medical applications.

Introduction to Genomics, and Medical and Statistical Genetics - a new course is being introduced by Professor Xiaohui Xie as part of the ICS Biomedical Computing undergraduate curriculum and will be offered campus-wide in 2012-2013 and cross listed with the Schools of Biological Sciences and Medicine.  This course will provide Teaching Assistant opportunities for BIT trainees, and improve the quality of internal BIT candidates.

*Course numbers are subject to change. Please refer to the most recent UCI General Catalog.

Laboratory Rotations

In addition to didactic training, laboratory rotations constitute an important component of the first-year program, providing students with intensive introductions to experimental design and quantitative data analysis, as well as introducing them to available research opportunities. Each quarter, each BIT Program student will conduct a rotation in the laboratory of a BIT faculty member, prior to choosing a primary thesis advisor at the end of the first year. Because of the interdisciplinary nature of the BIT Program and the diversity of the participating students, it is important that students become familiar with both “wet” experimental biology labs and computational labs. Therefore, students entering the program with a computational background are required to do one rotation in a biology laboratory and students with a biology background are required to do one rotation in a computational environment. Students are encouraged to pair up for interdisciplinary, collaborative work during their rotation experiences.

Choosing a BIT Faculty Thesis Advisor

Throughout the first two quarters of each year, BIT faculty will present informal “Pizza Seminars” describing their research interests to the BIT Program students. These presentations are a key mechanism by which students become familiar with various potential research areas prior to choosing research laboratory rotations and a thesis advisor. All first-year BIT Program students are required to attend these seminars and to select a primary thesis advisor at the end of the first year.

Continuing BIT Program Requirements

IGB and Home Department Seminars

All BIT students are required to attend seminars sponsored both by their home department and by the IGB. The IGB seminars and the IGB Distinguished Speaker Series most often emphasize computational aspects of biomedical informatics and computational biology. The home department seminars emphasize topics in the student’s primary area(s) of expertise.

BIT Lunch

In order to develop more of a program esprit de corps, trainees meet as a group the first Monday of each month for lunch. At these lunches the trainees are free to openly discuss their research projects and develop closer professional and personal ties with one another. The BIT lunch is facilitated by a BIT group Web site hosted by the trainees. At a typical BIT lunch, a biology trainee(s) might informally present their ongoing research, highlighting areas where they need bioinformatics assistance or input from computer scientists and/or computational biologists. At that point, the computation students might offer advice and explain the basis of computational methods and/or algorithms to address the problem. Often, appropriate algorithms or computational methods must be devised to deal with the problem. Sometimes the solutions are trivial, but at other times they develop into collaborations among the members of the group. Occasionally, the student’s invite BIT faculty or visiting scientists from other academic institutions or industry to discuss their interests with the group as well as host career development sessions.

Student Research Presentations

Each month, two program students are required to present a formal seminar to the training grant faculty and their research groups. This provides the students with the skills necessary for communicating their work to an interdisciplinary scientific audience. Every student in the program is required to present at least one seminar each year.

Annual Trainee Mini-Symposium

Each year in the spring, the Institute for Genomics and Bioinformatics sponsors an all day symposium for the trainees to present their research results. This has proven to be a very successful event. The students work very hard on their presentations. Each year this event has been very well attended by UCI faculty and student researchers from many disciplines across the UCI campus. The program and abstracts for past BIT Program Symposium are here.

Attendance and Participation in National Meetings

All students are encouraged to attend national meetings to broaden their perspectives of current topics and methods in biomedical informatics and computational biology research. Training grant and IGB travel support for those students presenting their research results at a national meeting is given top priority.

Universal Campus

The Universal Campus provides an infrastructure for organizing and deploying collaborative meetings, such as classes, research group meetings, and conferences in a virtual 3D world. Please visit Universal Campus for more information.