Biomolecular Engineering

2014-15 General Catalog

Baskin School of Engineering
335 Baskin Engineering Building
(831) 459-2158

Faculty | Course Descriptions

Program Description

The Department of Biomolecular Engineering is an interdisciplinary department that combines expertise from biology, mathematics, chemistry, computer science, and engineering to train students and develop technologies to address major problems at the forefront of biomedical and bio-industrial research. Students trained in the Department of Biomolecular Engineering can look forward to careers in academia, the information and biotechnology industries, public health, or medical sciences.

The department offers an undergraduate minor and a bachelor of science (B.S.) degree in bioinformatics, and graduate master of science (M.S.) and doctor of philosophy (Ph.D.) degrees in biomolecular engineering and bioinformatics. The department co-sponsors the B.S. in bioengineering program, described elsewhere in this catalog, with the departments of Computer Engineering, Electrical Engineering, and Molecular, Cell, and Developmental (MCD) Biology. The department co-sponsors the Program in Biomedical Science and Engineering (PBSE), a doctoral training program, with the departments of MCD Biology, Chemistry and Biochemistry, and Microbiology and Environmental Toxicology.

Departmental faculty advise undergraduate and graduate researchers enrolled in the bioinformatics, bioengineering, and related degree programs. Members of the Department of Biomolecular Engineering actively collaborate with faculty from other Baskin School of Engineering departments, such as Applied Mathematics and Statistics, Computer Engineering, Computer Science, and Electrical Engineering; and with the Physical and Biological Sciences departments of MCD Biology, Chemistry and Biochemistry, Microbiology and Environmental Toxicology, Ecology and Evolutionary Biology, and Ocean Sciences.

Bioinformatics Major

Bioinformatics combines mathematics, science, and engineering to explore and understand biological data from high-throughput experiments, such as genome sequencing, gene-expression chips, and proteomics experiments. The program builds upon the research and academic strengths of the faculty in the Center for Biomolecular Science and Engineering,

The Human Genome Project, the international collaboration to determine the sequence of human DNA and understand its function, had its origin in a conference that took place at UCSC in 1985. One notable output from our research is that UCSC is the primary release site for the public version of the human genome (, as well as the repository for the ENCODE (Encyclopedia Of DNA Elements) project, a national effort to annotate the entire human genome with multiple functional assays. We also have a strong research group in systems biology, functional genomic characterization of stem cells, and play a lead role in national efforts to discover molecular underpinnings of various cancers, including participating as a Dream Team for the Stand Up To Cancer project and a data-analysis center for The Cancer Genome Atlas project.

The undergraduate bioinformatics degree program prepares students for graduate school or a career in the pharmaceutical or biotechnology industries.

The immense growth of biological information stored in computerized databases has led to a critical need for people who can understand the languages, tools, and techniques of statistics, science, and engineering. A classically trained scientist may be unfamiliar with the statistical and algorithmic knowledge required in this field. A classically trained engineer may be unfamiliar with the chemistry and biology required in the field. Thus, this program strives for a balance of the two: an engineer focused on the problems of the underlying science or, conversely, a scientist focused on the use of engineering tools for analysis and discovery.

The undergraduate degree program in bioinformatics builds a solid foundation in the constituent areas of the field. Students complete core sequences in mathematics (including calculus, statistics, and discrete mathematics), science (including biology, chemistry, and biochemistry), and engineering (including programming, algorithms, and databases). The core topics are brought together in two bioinformatics courses: Biomolecular Engineering 110, Computational Biology Tools, and Biomolecular Engineering 205, Bioinformatics Models and Algorithms. Students have two electives for specialization within the fields of bioinformatics and are required to take Biomolecular Engineering 80G, Bioethics in the Twenty-First Century: Science, Business, and Society to study the ethical, legal, and social implications of this new technology.

Courses for Nonmajors

Biomolecular Engineering 5, Introduction to Biotechnology, presents a broad overview of the impact of biotechnology on the diagnosis and treatment of disease.

Biomolecular Engineering 160, Programming for Biologists and Biochemists, provides an introductory programming class using Python and BioPython to analyze, transform, and publish biological data.

Biomolecular Engineering 80G, Bioethics in the Twenty-First Century: Science, Business, and Society, is particularly appropriate to all students interested in the societal issues surrounding the revolutions in bioinformatics and biotechnology.

Biomolecular Engineering 110, Computational Biology Tools, provides an introduction to the tools and techniques of bioinformatics from a users view. It is intended for biologists and biochemists who need to use bioinformatics tools, but are not primarily interested in building new bioinformatics tools.

Biomolecular Engineering 130, Genomes Genome-scale analysis to answer biological questions.

Biomolecular Engineering 155, Biotechnology and Drug Development, examines the science and process of discovering, testing, and manufacturing new drugs within the pharmaceutical industry.

Bioinformatics Policies

Declaration of the Major

Admission to the bioinformatics major is based on the required lower-division courses: BIOL 20A, BIOE 20B, BME 80G, CHEM 1A, CHEM 1B/M, CHEM 1C/N, CMPE 16, CMPS 12A/L (or CMPS 5J and 11 OR CMPE 12/L and CMPE 13/L), CMPS 12B/M, MATH 19A, MATH 19B, MATH 23A, and fundamental upper-division courses: AMS 131, CHEM 108A/L, CHEM 108B/M, and CMPS 101. Students must have completed 50 credits from this list by the end of the fifth quarter. Students must also have a GPA of 2.8 or better in all attempts in these courses. Students changing major after the sixth quarter will need 10 additional credits for each additional quarter.

Denials of admission to the major may be appealed by submitting a letter to the School of Engineering Undergraduate Office, describing why the grade point average obtained is not an accurate reflection of the student’s potential, or requesting that other completed upper-division courses be considered in admissions process.

Courses Taken Elsewhere

Please refer to the School of Engineering section of the catalog for policies about taking courses at other institutions after enrolling at UCSC.

Honors in the Major

Bioinformatics majors are considered for "Honors in the Major" and "Highest Honors in the Major" based on their GPA and on results of undergraduate research. Students with a GPA of 3.7 receive "Highest Honors in the Major." Students with a GPA of 3.3 receive "Honors in the Major." Students with particularly significant accomplishments in undergraduate research may receive honors or highest honors with a lower GPA.  Students who have been found guilty of academic misconduct are not eligible for either honors or highest honors.

Transfer Students

Transfer students need eight transferable courses from the list of courses used for admission to the major for on-campus students, with a GPA in those courses of 2.8 or better. Students with fewer than 10 transferable courses may find it difficult to complete the major in only two more years.

School of Engineering Policies

Please refer to the School of Engineering section of the catalog for additional policies that apply to all School of Engineering programs.

Preparation for the Major

Students applying for admission to the bioinformatics major should have completed four years of high school mathematics (through advanced algebra and trigonometry) and three years of science, including one year of chemistry and one year of biology. Comparable college mathematics and science courses completed at other institutions may be accepted in place of high school preparation. Students without this preparation may be required to take additional courses to prepare themselves for the program.

Requirements of the Bioinformatics Major

Every bioinformatics major must have a faculty adviser, assigned by the Baskin School of Engineering undergraduate advising office, and with that adviser must formulate a program of proposed course work that meets the major requirements. Because of the enormous breadth of requirements, bioinformatics majors are urged to take honors courses or sections whenever possible to get as much as possible out of the courses they take in each field.

Lower-Division Requirements

Majors must complete the following lower-division courses:


Biology (BIOL) 20A, Cell and Molecular Biology

Biology (BIOE) 20B, Development and Physiology

Biomolecular Engineering

Biomolecular Engineering 80G, Bioethics in the Twenty-First Century: Science, Business, and Society


Chemistry 1A, 1B/M, and 1C/N, General Chemistry/Laboratory

Computer Engineering

Computer Engineering 16, Applied Discrete Mathematics

Programming 1

Computer Science 12A/L, Introduction to Programming/Laboratory (accelerated); or

Computer Science 5J, Introduction to Programming in Java, and 11, Intermediate Programming; or

Computer Engineering 12/L, Computer Systems and Assembly Language/Laboratory, and 13/L, Computer Systems and C Programming/Laboratory

Programming 2

Computer Science 12B/M, Introduction to Data Structures/Laboratory


Mathematics 20A-B, Honors Calculus; or

Mathematics 19A-B, Calculus for Science, Engineering, and Mathematics (Credit for one or both can be granted with adequate performance on the College Entrance Examination Board (CEEB) calculus AB or BC Advanced Placement examination.)

Mathematics 23A, Multivariable Calculus

Upper-Division Requirements

Majors must complete the following upper-division courses:

Applied Mathematics and Statistics

Applied Mathematics and Statistics 131, Introduction to Probability Theory

Applied Mathematics and Statistics 132, Statistical Inference

Biochemistry and Molecular Biology

Biochemistry 100A, Biochemistry (first in three-part sequence)


Biomolecular Engineering 110, Computational Biology Tools

Biomolecular Engineering 130, Genomes

Biomolecular Engineering 205, Bioinformatics Models and Algorithms

One of the following:

Biomolecular Engineering 211, Computational Systems Biology; or

Biomolecular Engineering 230/L, Computational Genomics/Laboratory; or

Biomolecular Engineering 195, Senior Thesis Research

Biology (BIOL)

Biology 105, Genetics


Chemistry 108A/L and 108B/M, Organic Chemistry/Laboratory; or

Computer Engineering

Computer Engineering 185, Technical Writing for Computer Engineers

Computer Science

Computer Science 101, Algorithms and Abstract Data Types

One of the following:

Computer Science 182, Introduction to Database Management Systems, or

Computer Science 180, Database Systems.

Advanced Programming

Computer Science 109, Advanced Programming

Required Electives

Students must select one additional course as an elective, justify their choice in writing, and get the choice approved by their faculty adviser. The following courses are typical of the ones chosen, but do not constitute a pre-approved list:

Applied Mathematics and Statistics 162

Biochemistry 100B, 100C, 110

Biology 105L, 105M, 109L, 110, 115, 115L, 117A, 117B, 140, 187L, 200A, 200B

Biomolecular Engineering 101/L, 102, 109, 128, 140, 150/L, 155, 177, 178, 211, 230

Computer Engineering 108, 177

Computer Science 104A, 105, 115, 116, 130, 140, 142, 160/L

Microbiology and Environmental Toxicology 119, 119L

Technology and Information Management 105, 206

Note: many of these courses are offered only once a year and have long prerequisite chains, so advance planning is necessary to make sure elective courses can be fit into the student's schedule.

Disciplinary Communication (DC) Requirement

Students of every major must satisfy that major's upper-division disciplinary communication (DC) requirement. Bioinformatics majors satisfy the DC requirement by completing Computer Engineering 185, Technical Writing for Engineers.

Comprehensive Requirement

The bioinformatics comprehensive requirement can be met by taking Biomolecular Engineering 211, Computational Systems Biology; or Biomolecular Engineering 230/L, Computational Genomics, which include substantial projects; or Biomolecular Engineering 195, Senior Thesis Research. Students electing the senior thesis must submit a written thesis proposal to the undergraduate director of bioinformatics for approval one quarter prior to submitting the final thesis.

Requirements of the Bioinformatics Minor

Where the bioinformatics major is intended for people who wish to become bioinformaticians and create the tools needed to solve new problems in computational biology, the bioinformatics minor is intended primarily for bioinformatics tool users who are majoring in a biological or chemical specialty. The bioinformatics minor is also appropriate for computer science or computer engineering majors who are considering graduate work in bioinformatics.

A bioinformatics minor consists of the following 16 courses:

Lower-division (10 courses)

Biology (2)

Biology 20A, Cell and Molecular Biology; and

Biology 20B, Development and Physiology

General chemistry (3)

Chemistry 1A, 1B/M, and 1C/N

Single-Variable Calculus (2)

Mathematics 19A and 19B (preferred); or

Mathematics 11A and 11B; or

Mathematics 20A and 20B

Programming 1 (1)

Computer Science 12A/L; or

Computer Science 5J and 11; or

Computer Engineering 12/L and 13/L

Programming 2 (1)

Biomolecular Engineering 160/L; or

Computer Science 12B/M

Bioethics (1)

Biomolecular Engineering 80G

Upper-division (6 courses)

Organic chemistry (1)

Chemistry 108A

Biochemistry (1)

Biochemistry 100A; or

Chemistry 103; or

Biology 100

Statistics (2)

Computer Engineering 107; or

Applied Mathematics and Statistics 131

Applied Mathematics and Statistics 132

Bioinformatics (1)

Biomolecular Engineering 110


Biochemistry 100B; or

any other upper-division or graduate biomolecular engineering course

The bioinformatics minor requirements may satisfy the requirements of other majors or minors under the campus policy discussed in Major and Minor Requirements. Majors with substantial overlap include biochemistry, bioengineering, all biology majors, chemistry, computer science, and computer engineering. Students pursuing one of these majors are particularly encouraged to consider the bioinformatics minor.

The Bioinformatics Combined B.S./Graduate Degree Program

Because our bioinformatics B.S. program provides excellent preparation for a graduate program in bioinformatics, we offer a combined B.S./graduate degree program that allows our B.S. students to complete the M.S. (or Ph.D.) somewhat sooner than students with a less tailored preparation.

The current B.S. and graduate requirements have four courses in common:

Biomolecular Engineering 80G, Bioethics in the 21st Century

Biomolecular Engineering 205, Bioinformatics Models and Algorithms

Biomolecular Engineering 230, Computational Genomics

Applied Mathematics and Statistics 206, Bayesian Statistics

The combined B.S./graduate degree program does not make any changes to the undergraduate program, except that students must pass the four overlapping courses listed above for a grade of B- or better.

The requirements at the graduate level are changed to remove the four courses that overlap with the B.S. and to add two graduate electives to be chosen by the students with the approval of their advisers. Thus, the total number of full courses required is reduced from nine to seven.

To apply for the combined program, students apply to the M.S. or Ph.D. program through the normal graduate admission process in the fall of their senior year. If admitted into the graduate program, they are automatically included in the combined B.S./M.S. or B.S./Ph.D. program.

Bioinformatics Major Planners

As in all engineering and science programs, it is recommended that students spread their general education requirements out over all 12 quarters. Students considering pursuing a bioengineering or bioinformatics degree should follow the biomolecular engineering concentration of the bioengineering B.S. program and complete the programming sequence (Computer Science 12A and 12B) by the end of their second year.

Four-year plans require individual design to fit in the desired electives, so only the first two years of the academic plan are presented here. It is recommended that students reserve the summer after the junior year for undergraduate research. One popular plan involves taking organic chemistry and the associated laboratories in the summer after completing general chemistry, so that biochemistry may be started in the junior year.

Biomolecular Engineering 205, Bioinformatics Models and Algorithms, should be taken after Biomolecular Engineering 110, Computational Biology Tools.

Sample Plan












college core

gen ed

gen ed









gen ed

gen ed

Biomolecular Engineering and Bioinformatics Graduate Program

The Department of Biomolecular Engineering offers interdisciplinary M.S. and Ph.D. degrees in biomolecular engineering and bioinformatics.

Course Requirements

Both masters and doctoral students must complete eight, 5-credit courses and one 3-credit research and teaching course. In addition, M.S. students must complete three seminar courses, while Ph.D. students must complete five seminar courses. M.S. students must also complete one lab rotation, and Ph.D. students must complete three research laboratory rotations (course 296) with different supervisors.

Core courses (5-credit) six are required

Bioinformatics Emphasis

  • BME 205, Bioinformatics Models and Algorithms

  • Two Biomolecular Engineering graduate courses from the bioinformatics list

  • One Biomolecular Engineering graduate course from the biomolecular engineering list

  • One graduate statistics course (Applied Mathematics and Statistics 206B recommended)

  • One graduate course from MCD Biology, Chemistry and Biochemistry, or Microbiology and Environmental Toxicology

Biomolecular Engineering Emphasis

  • BME 250, Molecular Biomechanics

  • Two Biomolecular Engineering graduate course from the biomolecular engineering list

  • One Biomolecular Engineering graduate courses from the bioinformatics list

  • Two graduate courses from Applied Mathematics and Statistics, MCD Biology, Chemistry and Biochemistry, or Microbiology and Environmental Toxicology

Ethics Course (5-credit) one is required

  • BME 80G, Bioethics in the Twenty-First Century: Science, Business, and Society

  • Sociology 268A, Science and Justice: Experiments in Collaboration.

Electives (5-credit) one is required

One graduate course consistent with the students degree objectives. With preapproval by the graduate director, this elective may be an upper-division undergraduate course selected to improve background in areas not studied as an undergraduate.

Independent or thesis research courses cannot be counted as electives.

Students must choose courses with faculty guidance and approval to balance their preparation and make up for deficiencies in background areas. With consent of the graduate director, variations in the composition of the required courses may be approved.

Other Curriculum Requirements

BME 200, Research and Teaching in Bioinformatics, 3 credits


M.S. students: a minimum of three seminar courses, including at least one quarter of the 2-credit Biomolecular Engineering seminar, 280B

Ph.D. students: a minimum of six seminar courses, including at least two quarters of the 2-credit Biomolecular Engineering seminar, 280B

Before and after advancement, full-time Ph.D. students are required to enroll in at least one seminar course each quarter (e.g., 280 or 281), and must present the results of their ongoing research at least once each year. Because the intent of the seminar requirement is to ensure breadth of knowledge, lab group meetings (BME 281 courses) do not count for the seminar requirement.

Research Experience

M.S. students: one laboratory rotation (BME 296), and one quarter of independent study (BME 297).

Ph.D. Students: three laboratory rotations (course 296), generally within the first 12 months. One of the laboratory rotations must be with a faculty supervisor who does wet-lab research, though the students rotation project may be purely computational.

Course Lists

The following are the bioinformatics and biomolecular engineering course lists. The lists are subject to change as courses and course content changes. The graduate office maintains the current list.

Bioinformatics list: 205, 211, 230, 235

Biomolecular Engineering list: 215, 250, 255

Qualifying Examinations

Ph.D. students are required to pass the qualifying examination and advance to candidacy by the end of their second year.

Adequate Progress

Graduate students receiving two or more U (unsatisfactory) grades or grades below B in courses relevant to the program are not making adequate progress and will be placed on academic probation for the next three quarters of registered enrollment.

Graduate students who fail (unsatisfactory or lower than B) a relevant course while on probation may be dismissed from the program. Students may appeal their dismissal. Graduate students who fail a relevant course after being removed from probation are immediately returned to academic probation.

Graduate students experiencing circumstances that may adversely affect their academic performance should consult with their adviser and the graduate director.

Masters Capstone Requirement

M.S. students must complete a one-quarter research project with written report to fulfill the capstone requirement. In consultation with the faculty adviser, the student forms a Master’s Capstone Reading Committee of at least two faculty members (including the adviser), each of whom is provided a copy of the project report. The final project report must be signed by the reading committee before the award of the Master of Science Degree.

Doctoral Dissertation Requirements

Ph.D. students must select a faculty research adviser by the end of the first year. A qualifying examination committee is then formed in the second year, which consists of the adviser and three additional members, and which is approved by the graduate director and the campus graduate dean. At least two of the four must be members of the Department of Biomolecular Engineering. The student must submit a written dissertation proposal to all members of the committee and the graduate program adviser one month in advance of the examination. The dissertation proposal is publicly and formally presented in an oral qualifying examination given by the qualifying committee.

Ph.D. candidates will submit the completed dissertation to a reading committee at least one month prior to the dissertation defense. The reading committee, formed upon advancement to candidacy, consists of the dissertation supervisor and two readers appointed by the graduate director upon the recommendation of the dissertation supervisor. At least one of the three must be a member of the Department of Biomolecular Engineering. The candidate will present his or her research in a public seminar. The seminar will be followed by a defense of the dissertation to the reading committee and attending faculty, who will then decide whether the dissertation is acceptable or requires revision.

Transfer Limitations

Up to two courses may be transferred from other graduate institutions with the approval of the faculty adviser and the graduate director.

[Return to Top]

Revised: 09/01/14