B.S. Computer Science with a Specialization in Bioinformatics (CSE-BS-003)

Updated June 26, 2026

Biomolecular data is rapidly transforming Modern Biology into a computational and data science. This one-of-a-kind major provides an opportunity for students to understand the sources of biomolecular data, instruments that generate the data, and the computational methods--- algorithms, machine learning, statistics, and databases---used to analyze the data and make biological discoveries. It is intended for students who would like to pursue careers in academia, healthcare, biotechnology, and data science companies.  

The explosion in biological knowledge spawned by the various genome projects has created entirely new fields and industries, and a need for trained computational biologists who are familiar with biology, mathematics, and computer sciences. The computer science and engineering department offers rigorous, interdisciplinary training in the new and rapidly evolving field of bioinformatics.

Bioinformatics refers to advanced computational and experimental methods that model the flow of information (genetic, metabolic, and regulatory) in living systems to provide an integrated understanding of the system properties of organisms.

This interdisciplinary major also is offered by the Division of Biological Sciences and the Department of Bioengineering

UCSD- CSE General Catalog

Degree Planning:

CSE-BS-003 Major Policies
  • All major requirements must be taken for a letter grade AND passed with a C- or better (with the exception of CSE-089, CSE-91, CSE-95, CSE-197, CSE-198 and CSE-199).
  • A maximum of 4 units of special studies coursework may count from the following: CSE-197, CSE-198, CSE-199, CSE-199H, ENG-100D, ENG-100DR, or ENG-100L
  • A maximum of 12 units of CSE-190 can be used towards Open CSE elective credit. May be repeated for credit max 3 times (maximum of 12 units; assuming courses taken for a different topic).
    • Please visit the CSE-190 website for current offerings and to view the tag for each course.
  • Undergraduate students may use CSE graduate-level courses towards their major requirements, but may need a petition if they have taken the equivalent/similar undergraduate course.
  • Undergraduate students must get instructor's permission and departmental approval (TEA request) to enroll in a graduate course.
  • CSE-291's are topics courses and are counted as part of the maximum of three CSE-190's allowed for CSE electives. 
  • Untagged upper division CSE courses that may be used as Open CSE Electives are CSE-109 (2 units), CSE-190 (tagged based on offering), CSE-192, CSE-195, CSE-197, CSE-198, CSE-199, CSE-199H. 

2026-2027 B.S. Computer Science with Bioinformatics Specialization Electives:

Computer Science and Engineering

Any upper-division CSE course between CSE-100 to 190, 193, 194 that is not being used for another major requirement (and is taken for a letter grade and passed with a C- or better) may be used towards an upper-division "CSE Elective".

Cognitive Science

COGS-108 - Data Science in Practice (4) - Applications of Computing

COGS-109 - Modeling and Data Analysis (4) - Applications of Computing

COGS-118A - Supervised Machine Learning Algorithms (4) - Applications of Computing

COGS-118B - Intro to Machine Learning II (4) - Applications of Computing

COGS-118C - Neural Signal Processing (4) - Applications of Computing

COGS-120 - Interaction Design (5) - Applications of Computing

COGS-121 - Human Computer Interaction Programming Studio (4) - Applications of Computing

COGS-122 - Startup Studio (4) - Applications of Computing

COGS-123 - Social Computing (4) - Applications of Computing

COGS-124 - HCI Technical Systems Research (4) - Applications of Computing

COGS-125 - Advanced Interaction Design (4) - Applications of Computing

COGS-126 - Human-Computer Interaction (4) - Applications of Computing

COGS-127 - Designing Human-Data Interactions (4) - Applications of Computing

COGS-181 - Neural Networks/Deep Learning (4)  - Applications of Computing

COGS-185 - Advanced Machine Learning Methods (4) - Applications of Computing

COGS-186 - Genetic Algorithms (4) - Applications of Computing

COGS-187A - Usability and Information Architecture (6) - Applications of Computing

COGS-187B - Practicum in Professional Web Design (4) - Applications of Computing

COGS-188 - Artificial Intelligence Algorithms (4) - Applications of Computing

COGS-189 - Brain Computer Interfaces (4) - Applications of Computing

Please use the Triton Enrollment Authorization (TEA) for COGS course clearance.

Data Science

DSC-100 - Introduction to Data Management (4) - Applications of Computing

DSC-102 - Systems for Scalable Analytics (4) - Systems

DSC-120 - Signal Processing for Data Analysis (4) - Systems

DSC-123A- Optimization Methods for Data Science I (4) - Theory

DSC-123B- Optimization Methods for Data Science II (4) - Theory

Design

DSGN-100 - Prototyping (4) - Applications of Computing

Economics

ECON-172A - Operations Research A (4) - Applications of Computing

ECON-172B - Operations Research B (4) - Applications of Computing

Education Studies

EDS-124AR - Teaching Computation in the Digital World  (4) - Applications of Computing

EDS-124BR -  Teaching Computational Thinking for Everyone (4) - Applications of Computing

Electrical & Computer Engineering (ECE)

ECE-111 - Advanced Digital Design Project (4) - Systems

ECE-140A - The Art of Product Engineering I (4) - Systems or Applications of Computing

ECE-140B - The Art of Product Engineering II (4) - Systems or Applications of Computing

Engineering (Global Ties)

ENG-100D(R)/ENG-100L: Principles of Team Engineering: globalties.ucsd.edu

  • Students may use up to 4 units of ENG 100D/ENG 100L courses towards upper division CSE Elective credits (as part of the 4 units maximum of CSE 198/199/199H Special Studies courses allowed). You are NOT able to take ENG 100D twice.
  • Students must take ENG 100L twice (2 units each time) to receive credit for upper division CSE Elective (not exceeding the 4 units of CSE 198/199/199H Special Studies courses)
  • Students may request to have their degree audit updated by contacting the Virtual Advising Center.
Linguistics

LIGN-165 - Computational Linguistics (4) - Applications of Computing

LIGN-167 - Deep Learning for Natural Language Understanding (4) - Applications of Computing

Mathematics

MATH-114 - Introduction to Computational Stochastics (4) - Applications of Computing

MATH-155A - Geometric Computer Graphics (4) - Applications of Computing

MATH-170A - Introduction to Numerical Analysis: Linear Algebra (4) - Theory

MATH-170B - Introduction to Numerical Analysis: Approximation and Nonlinear Equations (4) - Theory

MATH-170C - Introduction to Numerical Analysis: Ordinary Differential Equations (4) - Theory

MATH-171A - Introduction to Numerical Optimization: Linear Programming (4) - Theory

MATH-171B - Introduction to Numerical Optimization: Nonlinear Programming (4) - Theory

MATH-173A - Optimization Methods for Data Science I (4) - Theory

MATH-173B - Optimization Methods for Data Science II (4) - Theory

MATH-181D - Statistical Learning (4) - Theory

MATH-185 - Introduction to Computational Statistics (4) - Theory

MATH-187A - Introduction to Cryptography (4) - Theory

MATH-189 - Exploratory Data Analysis and Inference (4) - Applications of Computing

Music

MUS-171 - Computer Music I (4) - Applications of Computing

MUS-172 - Computer Music ll (4) - Applications of Computing

MUS-177 - Music Programming (4) - Applications of Computing

Visual Arts

VIS-141A - Computer Programming for the Arts I (4) - Applications of Computing

VIS-141B - Computer Programming for the Arts II (4) - Applications of Computing

__________________________________________

Four Year Plans:

  • Academic Planning Worksheet (link to copy a Google Sheet): blank worksheet for students to be able to create a sample long term plan which can be brought to an advising meeting 

  • Sample Plans By College: sample long term plan that includes college requirements

Sample 4-year Plan
Year Fall Winter Spring

First Year

CSE-008A*1 or CSE-011*1

MATH-020A

CHEM-006A

LDE

CSE-011*1

CSE-020*2

MATH-020B

CHEM-006B

MATH-020C

BILD-001

CSE-012

CSE-029

Second Year

CSE-030

CSE-021*3

CHEM-040A or CHEM-041A

BILD-004

CSE-100

CHEM-040B or CHEM-041B or BENG-120*4

MATH-018

 

CSE-101

BILD-003

PHYS-002A

 

Third Year

BICD-100

BIMM-100

CSE Elective

 

BIMM-101

MATH-186

Biochemistry

 

CSE-182

CSE Elective

 

Fourth Year

BENG-183

CSE Elective

CSE Elective

CSE-181

CSE Elective

 

CSE-185

 

 

 

*1: Students who do not have programming experience should begin with the two-track course: CSE 8A (take CSE 11 in the second quarter). Students who have programming experience may begin with CSE 11 (take CSE 12 and CSE 29 in the second quarter).

*2: CSE 20  is not required for major requirements but recommended to complete for CSE 21 prerequisites. If you want to bypass the CSE 20 to enroll in CSE 21, please submit an Triton Enrollment Authorization (TEA) request.

*3:  CSE 21 may be substituted with MATH 154 or MATH 184 or MATH 188* This is a manual update an advisor needs to make. Send a message through the Virtual Advising Center (VAC)

*4: CHEM 40B or CHEM 41B or BENG 120 is not required for major requirements, but must be completed for BIMM 100/BIBC 102 prerequisites.

CSE Electives: Students are permitted to take any of these pre-approved courses to fulfill their CSE Elective requirements. Please note that courses on this list may not automatically populate in the correct area of a student's degree audit. In order to update the audit, please contact the CSE major advisors through the Virtual Advising Center (VAC). 

Major restrictions - The following majors may NOT double major or minor in CSE: 

- Any majors that fall under the Jacob's School of Engineering

- Data Science majors

- Math-Computer Science majors 

Transfer Students:

​Transfer students are in a special situation where the credits they come in with vary vastly from one student to another. To assist transfer students with their long term plans for completing major requirements, we have created different long term plans with different entry points depending on the CSE credits students typically come in with. These plans only include CSE major requirements, for questions regarding your college and university requirements please check with your college.

*These plans only focus on CSE coursework. For a list of all CSE Major requirements (including math and general science courses needed), please see the BS Computer Science with Specialization in Bioinformatics (CSE-BS-003)  Checklist above. 


Incoming Computer Science with a Specialization in Bioinformatics majors with transfer credit for CSE-011, CSE-012, and CSE-020, click here for a sample long-term plan. 
Fall Quarter - First Year Winter Quarter - First Year Spring Quarter - First Year
CSE-021 CSE-030 CSE-100
CSE-029  CHEM-040A or CHEM-041A CHEM-040B or CHEM-041B or BENG-120
CHEM-006B BILD-003 BILD-004
LDE   MATH-186
Fall Quarter - Second Year Winter Quarter - Second Year Spring Quarter - Second Year
BICD-100 CSE-181 CSE-182
BIMM-100 BIMM-101 CSE-185
Biochemistry BENG-183 CSE Elective
CSE-101    
Fall Quarter - Third Year Winter Quarter - Third Year  
CSE Elective CSE Elective  
CSE Elective CSE Elective  
     
     

 

Incoming Computer Science with a Specialization in Bioinformatics majors with transfer credit for CSE-011, CSE-012, CSE-020, and CSE-030, click here for a sample long-term plan. 
Fall Quarter - First Year Winter Quarter - First Year Spring Quarter - First Year
CSE-021 CSE-100 CSE-101
CSE-029 CHEM-040A or CHEM-041A CHEM-040B or CHEM-041B or BENG-120
CHEM-006B BILD-003 BILD-004
LDE   MATH-186
Fall Quarter - Second Year Winter Quarter - Second Year Spring Quarter - Second Year
BICD-100 CSE-181 CSE-185
BIMM-100 BIMM-101 CSE-182
Biochemistry BENG-183 CSE Elective
     
Fall Quarter - Third Year Winter Quarter - Third Year  
CSE Elective CSE Elective  
CSE Elective CSE Elective