ucsd biology phd program

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What is Quantitative Biology (qBio)?

Quantitative biology (qBio) is a fusion of biological and physical sciences, with the goal to predict and understand living systems in quantitative terms , including their behaviors, interactions, and heredity. qBio combines the power of abstract, quantitative reasoning with advanced instrumentation from physics and engineering to discover fundamental organizing principles of living systems .

Thus, the next generation of quantitative biologists need to master three skills:

• identify key unsolved biological phenomena
• carry out relevant quantitative measurements
• develop theory to understanding biological systems

PhD students in the qBio program at UC San Diego master these skills and use them to understand biological phenomena across scales: from molecules, to physiology of unicellular and multicellular organisms, to populations.

Learn more about the qBio PhD specialization .

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Find Your Degree Program

We offer a wide variety of academic and professional graduate degree programs and we welcome talented prospective students from across the nation and around the world to apply for admission.

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Halıcıoğlu data science institute.

• Data Science
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Jacobs School of Engineering

• Architecture-Based Enterprise Engineering Systems
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• Chemistry & Biochemistry
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• Biostatistics
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• Anthropology
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• Scripps Institute of Oceanography

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Marine Biology (MB)

Interested in applying to our MS or PhD programs? View presentations from this year's info sessions .

Information for the Marine Biology PhD program and Master's degree programs

The program offers two tracks, Marine Biology and Marine Chemical Biology:

Marine Biology  (MB) is the study of marine organisms and their relationship with the physical and chemical dynamics of the marine environment. Faculty expertise encompasses several major areas of modern biology including evolutionary, ecological, organismic, physiological, biochemical, and genetic processes of marine animals and microorganisms.

Examples of current research activities include:

• Marine microbiology
• Algae biofuels and biotechnology
• Genomics, metagenomics, and bioinformatics
• Cell and developmental biology
• Physiology and biochemistry of marine animals
• Biomechanics and biomaterials
• Ecotoxicology
• Photobiology
• Parasitology
• Animal behavior and behavioral ecology
• Deep-sea biology
• Phylogeny and taxonomy of marine animals
• Biogeography or marine populations
• Evolutionary genomics and molecular ecology of marine organisms
• Biodiversity, ecology, and conservation of marine ecosystems

Studies ranging from spatial ecology of coral reef ecosystems to the role of the marine microbiome in food web dynamics are being investigated in over thirty independent research laboratories. 

Marine Chemical Biology (MCB) is an interfacial discipline combining the fields of chemistry and biology to study and manipulate biological systems with the use of chemical, biochemical and genetic techniques and tools. Currently most of the investigations in the MCB track are focused on the discovery and application of marine microbial natural products and the study of biochemical processes utilized to create these unique molecules.

Marine natural products are amongst some of the most structurally novel in the natural world, and their chemical description is critical to developing their full biomedical and biotechnological value as well as exploring their functional roles in our natural world. Understanding the biosynthesis of these marine natural products by a combination of organic chemistry and recombinant biology approaches lays the foundation for the discovery and application of novel biosynthetic enzymes and the rational metabolic engineering of designer molecules. Some of these metabolites may have utility as biological reagents, pharmaceuticals, agrochemicals, biofuels, or other commodity chemicals. Innovative analytical methods are also being utilized to probe the sites of natural products’ biosynthesis in complex associations of marine species, including those involved in symbiotic relationships.

Potential advisors for prospective applicants

Prospective PhD and MS applicants should reach out to all potential advisors based on research interests to ascertain whether they are encouraged to apply. Additionally, PhD program applicants should be aware that funding for PhD students is usually supplied by individual advisors and that such funding is often very limited; hence, securing outside fellowships (e.g., the NSF GRFP) greatly increases the chance of admission.  See here for more information concerning funding.

Educational Requirements for Admission

In addition to the general requirements for admission to the PhD program listed  here , a major in one of the biological sciences (or equivalent), with basic course work in botany, microbiology, or zoology, as well as two years of chemistry, including organic chemistry, is required.  

Training in one or more of the following areas is strongly recommended: cellular biology, molecular biology, comparative physiology, genetics, developmental biology, ecology, evolutionary biology, vertebrate and invertebrate zoology, microbiology, and/or botany.

MB Applicant evaluation criteria

Factors that are used to evaluate applicants include, but are not limited to, (1) Academic preparation; (2) Scholarly potential; (3) Diversity, equity, and inclusion contributions; (4) Alignment with the program (i.e., fit with the laboratories of prospective advisors); (5) Realistic self-appraisal; and (6) Long-term goals.

If an OBP applicant decides to submit the entirely optional general GRE scores, those scores will be used similarly to the GPA, alongside the applicant’s other materials to inform the holistic assessment of the applicant’s “scholarly potential.”

We reemphasize that a requirement for the acceptance of even excellent applicants is the interest and ability of the prospective main advisor(s) to take on the student; the ability of even an interested advisor to admit is ultimately contingent on the availability of funding, whether from internal or external sources.

Programs of Study for PhD

Students admitted to Ocean Bioscience Program (OBP) are assigned an advisor, who is a chair of the three-person guidance committee. Students are assigned to a curricular group based on their interests. Although students may change curricular groups near the beginning of the year, they must commit to a curricular group early on because this determines which departmental exam they will take. During the year, students may be supported in a variety of ways. After the first year, the guidance committee is dissolved and the research advisor, and eventually the dissertation committee, provide guidance.

Marine Biology Curriculum:

Graduate students are expected to gain research experience in one or more laboratories during their first year.

Graduate students are required to complete SIO core courses including SIO 210, Physical Oceanography, SIO 260, Marine Chemistry, and SIO 280, Biological Oceanography.  In addition, students are also expected to enroll in SIOB 297 Marine Biology Seminar, the weekly marine biology seminar series, every quarter.   In the spring term of their first year at SIO, students will take a departmental exam consisting of a presentation of their first-year research in the form of a paper and short talk to the curricular group, followed by a meeting with their first-year advisory committee. MB Ph.D. students also must take at least two graduate-level marine organismal courses or labs. A partial list of courses that fulfill this requirement include: SIOB 271 Marine Zooplankton, SIOB 274 Natural History Below the Tides, SIOB 277 Deep Sea Biology, SIOB 281 Marine Physiology, SIOB 282 Phytoplankton Diversity, SIOB 283 Phycology: Marine Plant Biology, SIOB 284 Marine Invertebrates, SIOB 287A Marine Microbial Ecology, SIOB 293 Applications of Phylogenetics, SIOB 294 Biology of Fishes, and SIOB 296 Marine Tetrapods.

After their first year, students are expected to enroll and actively participate in at least one seminar course (SIO 278, 296, or equivalent) per year that will provide in-depth knowledge and reading in selected areas, as well as practice presenting scientific material.  Students frequently take additional SIO and UC San Diego School of Biological Sciences courses based on their research interests and general scientific education.

In addition to the seminar requirement discussed above, second-year students will present their research in a special Marine Biology mini-symposium, held in spring quarter; students in the second through fourth years are expected to participate in the research presentation class (SIO 291) each year. 

Marine Chemical Biology Curriculum:  

Graduate students are required to complete SIO core courses including SIO 210, Physical Oceanography, SIO 260, Marine Chemistry, and SIO 280, Biological Oceanography. In addition, students are required to enroll in SIOB 262 Marine Chemical Biology Seminar every quarter.  In the spring term of their first year at SIO, students will take a departmental exam consisting of a presentation of their first-year research in the form of a paper and short talk to the curricular group, followed by a meeting with their first-year guidance committee. 

Marine Chemical Biology graduate students are expected to gain research experience in one or more laboratories during their first year.  Additional courses that are recommended as electives in this Track, the exact composition of which will be decided by discussion between the student and the student’s first year guidance committee, include CHEM 257, Bioorganic and Natural Products Chemistry, SIO 242A-B, Marine Biotechnology I and II, SIO 264, Special Topics in Marine Natural Products Chemistry, and at least one of the following two courses: CHEM 254, Mechanisms of Organic Reactions and/or CHEM 258, Applied Spectroscopy. These are typically taken over the first two years of study. Additional electives, seminar courses, and special topics courses in graduate science and oceanography are available.

Second-year students will present their research along with students in the Marine Biology mini-symposium which is held in spring quarter.

Program of Study for MS

Required course work-.

• SIOC 210. Physical Oceanography (4 units)
• SIOG 260. Marine Chemistry (4 units)
• SIOB 280. Biological Oceanography (4 units)
• MB M.S. students also must take at least two graduate-level marine organismal courses or labs. A partial list of courses that fulfill this requirement include: SIOB 271 Marine Zooplankton, SIOB 274 Natural History Below the Tides, SIOB 277 Deep Sea Biology, SIOB 281 Marine Physiology, SIOB 282 Phytoplankton Diversity, SIOB 283 Phycology: Marine Plant Biology, SIOB 284 Marine Invertebrates, SIOB 287A Marine Microbial Ecology, SIOB 293 Applications of Phylogenetics, SIOB 294 Biology of Fishes, and SIOB 296 Marine Tetrapods

Elective course work-

Students may fulfill the remaining units of required course work through elective course offerings that may be recommended by the guidance committee.

Marine Chemical Biology Curriculum:

• SIOG 260. Marine Chemistry (4 units)
• SIOB 280. Biological Oceanography (4 units)

Students may fulfill the remaining units of required course work through elective course offerings selected in consultation with the students’ guidance committee. Typical recommended electives are below:

• Chem 257. Bioorganic and Natural Products Chemistry (4 units)
• SIOG 232. Ethical and Professional Science (2 units) or equivalent
• SIOB 242 A-B. Marine Biotechnology I and II (8 units)
• SIOB 264. Special Topics in Marine Natural Products Chemistry (3 units)
• Select at least one of the following: Chem 254. Mechanisms of Organic Reactions (4 units) and/or Chem 258. Applied Spectroscopy (4 units)

Research in Marine Biology

Marine Biology Faculty and Researchers:

• Octavio Aburto
• Andrew Allen
• Lihini Aluwihare
• Dahiana Arcila
• Douglas Bartlett
• Tarik Benmarhnia
• Ricardo Betancur
• Jeff S. Bowman
• Ronald Burton
• Dimitri Deheyn
• Terry Gaasterland
• Bill Gerwick
• Jack Gilbert
• Amro Hamdoun
• Ryan Hechinger
• Paul Jensen
• Linda Kelly
• James Leichter
• April Lukowski
• Deirdre Lyons
• Bradley Moore
• Richard Norris
• Brian Palenik
• Paul Ponganis
• Kim Prather
• Stuart Sandin
• Brice Semmens
• Jennifer Smith
• George Sugihara
• Jennifer Taylor
• Martin Tresguerres
• Lisa Zeigler

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Graduate Degrees Offered, 2023–24

Anthropology.

• Anthropology PhD*
• Anthropology and Cognitive Science PhD
• Anthropology (Science Studies) PhD
• Anthropology with a Specialization in Anthropogeny PhD
• Anthropology with a Specialization in Computational Social Science PhD
• Anthropology with a Specialization in Critical Gender Studies PhD
• Anthropology with a Specialization in Interdisciplinary Environmental Research PhD
• Audiology (Joint with San Diego State University) AuD

BIOENGINEERING

• Bioengineering MEng, MS, PhD
• Engineering Sciences (Bioengineering) (Joint with San Diego State University) PhD
• Bioengineering with a Medical Specialization MS
• Bioengineering with a Specialization in Medical Device Engin eering MEng
• Bioengineering with a Specialization in Bioinformatics PhD
• Bioengineering with a Specialization in Computational Neuroscience PhD
• Bioengineering with a Specialization in Multiscale Biology PhD
• Bioengineering with a Specialization in Quantitative Biology PhD

BIOINFORMATICS AND SYSTEMS BIOLOGY

• Bioinformatics and Systems Biology PhD
• Bioinformatics and Systems Biology with a Specialization in Biomedical Informatics PhD
• Bioinformatics and Systems Biology with a Specialization in Quantitative Biology PhD

BIOLOGICAL SCIENCES

• Biology MS,† PhD
• Biology (Joint with San Diego State University) PhD
• Biology with a Specialization in Anthropogeny PhD
• Biology with a Specialization in Bioinformatics PhD
• Biology with a Specialization in Biology Education Research MS †
• Biology with a Specialization in Immunology PhD
• Biology with a Specialization in Interdisciplinary Environmental Research PhD
• Biology with a Specialization in Multiscale Biology PhD
• Biology with a Specialization in Quantitative Biology PhD

BIOMEDICAL SCIENCES

• Biomedical Sciences PhD
• Biomedical Sciences with a Specialization in Anthropogeny PhD
• Biomedical Sciences with a Specialization in Bioinformatics PhD
• Biomedical Sciences with a Specialization in Immunology PhD
• Biomedical Sciences with a Specialization in Multiscale Biology PhD
• Biomedical Sciences with a Specialization in Quantitative Biology PhD

BIOSTATISTICS

• Biostatistics MS
• Biostatistics PhD

CHEMISTRY AND BIOCHEMISTRY

• Biochemistry and Molecular Biophysics, MS, PhD
• Chemistry MS, PhD
• Chemistry (Joint with San Diego State University) PhD
• Chemistry with a Specialization in Bioinformatics PhD
• Chemistry with a Specialization in Computational Science PhD
• Chemistry with a Specialization in Interdisciplinary Environmental Research PhD
• Chemistry with a Specialization in Multiscale Biology PhD
• Chemistry with a Specialization in Quantitative Biology PhD
• Classics (Tri-Campus Program with UC Irvine and UC Riverside) PhD

CLINICAL PSYCHOLOGY

• Clinical Psychology (Joint with San Diego State University) PhD
• Clinical Psychology and Cognitive Science (Joint with San Diego State University) PhD

CLINICAL RESEARCH

• Clinical Research MAS

COGNITIVE SCIENCE

• Cognitive Science PhD*
• Cognitive Science with a Specialization in Anthropogeny PhD
• Cognitive Science with a Specialization in Computational Social Science PhD
• Cognitive Science with a Specialization in Human-Centered Design PhD

COMMUNICATION

• Communication PhD*
• Communication (Science Studies) PhD
• Communication and Cognitive Science PhD
• Communication with a Specialization in Computational Social Science PhD
• Communication with a Specialization in Critical Gender Studies PhD

COMPARATIVE STUDIES IN LANGUAGE, SOCIETY, AND CULTURE

• Comparative Studies in Language, Society, and Culture PhD

COMPUTATIONAL SCIENCE, MATHEMATICS, AND ENGINEERING

• Computational Science, Mathematics, and Engineering MS

COMPUTATIONAL SOCIAL SCIENCE

• Computational Social Science MS

COMPUTER SCIENCE AND ENGINEERING

• Computer Science MS, PhD
• Computer Science with a Specialization in Human-Centered Design MS, PhD
• Computer Science (Computer Engineering) MS, PhD
• Computer Science (Computer Engineering) with a Specialization in Human-Centered Design PhD
• Computer Science and Cognitive Science PhD
• Computer Science with a Specialization in Bioinformatics PhD
• Computer Science and Engineering (Advanced Manufacturing) MS
• Computer Science and Engineering with a Specialization in Computational Science PhD
• Data Science and Engineering MAS
• Wireless Embedded Systems MAS

DATA SCIENCE

• Data Science MS, PhD
• Data Science (Online) MDSO
• Economics PhD*
• Economics with a Specialization in Computational Social Science PhD
• Economics with a Specialization in Interdisciplinary Environmental Research PhD

EDUCATION STUDIES

• Education MEd, PhD
• Education with a Specialization in Critical Gender Studies PhD
• Education Studies with a Specialization in Computational Social Science PhD
• Educational Leadership (Joint with California State University, San Marcos) EdD
• Teaching and Learning (Curricular Design) MA
• Teaching and Learning: Bilingual Education (ASL-English) MA

ELECTRICAL AND COMPUTER ENGINEERING

• Electrical and Computer Engineering (Advanced Manufacturing) MS
• Electrical Engineering (Applied Electromagnetics) MS, PhD
• Electrical Engineering (Applied Ocean Sciences) MS, PhD
• Electrical Engineering (Applied Physics) MS, PhD
• Electrical Engineering (Communication Theory and Systems) MS, PhD
• Electrical Engineering (Computer Engineering) MS, PhD
• Electrical Engineering (Electronic Circuits and Systems) MS, PhD
• Electrical Engineering (Intelligent Systems, Robotics, and Control) MS, PhD
• Electrical Engineering (Machine Learning and Data Science) MS, PhD
• Electrical Engineering (Medical Devices and Systems) MS, PhD
• Electrical Engineering (Medical Imaging) MS, PhD
• Electrical Engineering (Nanoscale Devices and Systems) MS, PhD
• Electrical Engineering (Photonics) MS, PhD
• Electrical Engineering (Signal and Image Processing) MS, PhD
• Engineering Sciences (Electrical and Computer Engineering) (Joint with San Diego State University) PhD

ETHNIC STUDIES

• Ethnic Studies PhD*
• Ethnic Studies with a Specialization in Computational Social Science PhD
• Ethnic Studies with a Specialization in Critical Gender Studies PhD
• Ethnic Studies with a Specialization in Interdisciplinary Environmental Research PhD

GLOBAL HEALTH

• Global Health, MA

GLOBAL POLICY AND STRATEGY, SCHOOL OF

• Chinese Economic and Political Affairs MCEPA
• International Affairs MAS, MIA
• Public Policy MPP
• History MA, PhD
• History (Judaic Studies) MA
• History (Science Studies) PhD
• History with a Specialization in Critical Gender Studies PhD

INTERDISCIPLINARY RESEARCH ON SUBSTANCE USE

• Interdisciplinary Research on Substance Use (Joint with San Diego State University) PhD

LANGUAGE AND COMMUNICATIVE DISORDERS

• Language and Communicative Disorders (Joint with San Diego State University) PhD

LATIN AMERICAN STUDIES

• Latin American Studies MA
• Latin American Studies (Cultural Studies) MA
• Latin American Studies (Gender Studies) MA
• Latin American Studies (History) MA
• Latin American Studies (International Migration) MA
• Latin American Studies (Sociology) MA

LEADERSHIP OF HEALTHCARE ORGANIZATIONS

• Leadership of Healthcare Organizations MAS

LINGUISTICS

• Linguistics PhD*
• Linguistics and Cognitive Science PhD
• Linguistics with a Specialization in Anthropogeny PhD
• Linguistics with a Specialization in Computational Social Science PhD
• Literature PhD*
• Literature with a Specialization in Critical Gender Studies PhD
• Writing MFA

MANAGEMENT, RADY SCHOOL OF

• Business Administration MBA
• Business Analytics MS
• Management PhD
• Management with a Specialization in Interdisciplinary Environmental Research PhD
• Professional Accountancy MPAc

MATERIALS SCIENCE AND ENGINEERING

• Materials Science and Engineering MS, PhD
• Materials Science and Engineering with a Specialization in Multiscale Biology PhD

MATHEMATICS

• Mathematics MA, PhD
• Mathematics (Applied) MA
• Mathematics with a Specialization in Bioinformatics PhD
• Mathematics with a Specialization in Computational Science PhD
• Mathematics with a Specialization in Statistics PhD
• Statistics MS

MATHEMATICS AND SCIENCE EDUCATION

• Mathematics and Science Education (Joint with San Diego State University) PhD

MECHANICAL AND AEROSPACE ENGINEERING

• Convergent Systems Engineering with a Specialization in Architecture-Based Enterprise Systems MAS
• Convergent Systems Engineering with a Specialization in Value Supply Chains MAS
• Convergent Systems Engineering with a Specialization in Cyber-Physical Social Systems MAS
• Engineering Sciences (Aerospace Engineering) MS, PhD
• Engineering Sciences (Applied Mechanics) MS, PhD
• Engineering Sciences (Mechanical and Aerospace Engineering) (Joint with San Diego State University) PhD
• Engineering Sciences (Applied Ocean Science) MS, PhD
• Engineering Sciences (Engineering Physics) MS, PhD
• Engineering Sciences (Mechanical Engineering) MS, PhD
• Engineering Sciences with a Specialization in Computational Science PhD
• Engineering Sciences with a Specialization in Multiscale Biology PhD
• Medical Devices Engineering MAS
• Contemporary Music Performance DMA
• Music with a Specialization in Critical Gender Studies PhD

NANOENGINEERING

• Chemical Engineering MS, PhD
• Chemical Engineering with a Specialization in Multiscale Biology PhD
• NanoEngineering MS, PhD
• NanoEngineering with a Specialization in Multiscale Biology PhD

NEUROSCIENCES

• Neurosciences PhD*
• Neurosciences and Cognitive Science PhD
• Neurosciences with a Specialization in Anthropogeny PhD
• Neurosciences with a Specialization in Computational Neuroscience PhD*
• Neurosciences with a Specialization in Multiscale Biology PhD

OCEANOGRAPHY, SCRIPPS INSTITUTION OF

• Climate Science and Policy MAS
• Earth Sciences MS, PhD
• Earth Sciences with a Specialization in Interdisciplinary Environmental Research PhD
• Geophysics (Joint with San Diego State University) PhD
• Marine Biodiversity and Conservation MAS
• Marine Biology MS, PhD
• Marine Biology with a Specialization in Interdisciplinary Environmental Research PhD
• Oceanography MS, PhD
• Oceanography with a Specialization in Interdisciplinary Environmental Research PhD

PHARMACY, SKAGGS SCHOOL OF

• Drug Development and Product Management MS
• Philosophy PhD*
• Philosophy (Science Studies) PhD
• Philosophy and Cognitive Science PhD
• Philosophy with a Specialization in Interdisciplinary Environmental Research PhD
• Astronomy PhD*
• Physics MS, PhD
• Physics (Biophysics) PhD
• Physics with a Specialization in Bioinformatics PhD
• Physics with a Specialization in Computational Neuroscience PhD
• Physics with a Specialization in Computational Science PhD
• Physics with a Specialization in Materials Physics MS
• Physics with a Specialization in Multiscale Biology PhD
• Physics with a Specialization in Quantitative Biology PhD

POLITICAL SCIENCE

• Political Science PhD*
• Political Science and International Affairs PhD
• Political Science with a Specialization in Computational Social Science PhD
• Political Science with a Specialization in Interdisciplinary Environmental Research PhD
• Political Science and International Affairs with a Specialization in Computational Social Science PhD
• Political Science and International Affairs with a Specialization in Interdisciplinary Environmental Research PhD
• Experimental Psychology PhD*
• Experimental Psychology and Cognitive Science PhD
• Experimental Psychology with a Specialization in Anthropogeny PhD
• Experimental Psychology with a Specialization in Computational Social Science PhD
• Experimental Psychology with a Specialization in Critical Gender Studies PhD

PUBLIC HEALTH

• Public Health (Epidemiology) (Joint with San Diego State University) PhD
• Public Health (Epidemiology) with a Specialization in Human-Centered Design (Joint with San Diego State University) PhD
• Public Health (Global Health) (Joint with San Diego State University) PhD
• Public Health (Global Health) with a Specialization in Human-Centered Design (Joint with San Diego State University) PhD
• Public Health (Health Behavior) (Joint with San Diego State University) PhD
• Public Health (Health Behavior) with a Specialization in Human-Centered Design (Joint with San Diego State University) PhD
• Public Health MPH
• Public Health with a Specialization in Human-Centered Design MPH
• Sociology PhD*
• Sociology (Science Studies) PhD
• Sociology and Cognitive Science PhD
• Sociology with a Specialization in Computational Social Science PhD
• Sociology with a Specialization in Critical Gender Studies PhD
• Sociology with a Specialization in Interdisciplinary Environmental Research PhD

STRUCTURAL ENGINEERING

• Geotechnical Engineering MS
• Structural Engineering MS, PhD
• Engineering Sciences (Structural Engineering) (Joint with San Diego State University) PhD
• Structural Engineering with a Specialization in Structural Health Monitoring and Non-Destructive Evaluation MS
• Structural Engineering with a Specialization in Computational Science PhD

THEATRE AND DANCE

• Drama and Theatre (Joint Program with UC Irvine) PhD
• Drama and Theatre with a Specialization in Critical Gender Studies (Joint with UC Irvine) PhD
• Theatre and Dance (Acting) MFA
• Theatre and Dance (Dance Theatre) MFA
• Theatre and Dance (Design) MFA
• Theatre and Dance (Directing) MFA
• Theatre and Dance (Playwriting) MFA
• Theatre and Dance (Stage Management) MFA

VISUAL ARTS

• Art History, Theory and Criticism PhD*
• Art History, Theory and Criticism with a Concentration in Art Practice PhD
• Art History, Theory and Criticism with a Specialization in Anthropogeny PhD
• Art History, Theory and Criticism with a Concentration in Art Practice and a Specialization in Anthropogeny PhD
• Art History, Theory and Criticism with a Specialization in Critical Gender Studies PhD
• Art History, Theory and Criticism with a Concentration in Art Practice and a Specialization in Critical Gender Studies PhD
• Art H istory, Theory and Criticism with a Specialization in Interdisciplinary Environmental Research PhD
• Art History, Theory and Criticism with a Concentration in Art Practice and a Specialization in Interdisciplinary Environmental Research PhD
• Visual Arts MFA

*The master’s degree may be awarded to students pursuing work toward the PhD after fulfillment of the appropriate requirements. See appropriate section of catalog.

†UC San Diego undergraduates in the junior or senior year may apply to their respective departments for admission to the integrated BS/MS degree program. A similar program is available to UC San Diego undergraduates in several of the engineering and science specialties. Consult department personnel and/or catalog departmental listing for complete information.

‡Pending approval.

^^Pending WSCUC approval.

Students who have completed some graduate study at UC San Diego and have been admitted to a doctoral program may apply to several interdisciplinary programs. See appropriate section of the General Catalog .

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Education & Training

Phd in bioinformatics and systems biology with emphasis in biomedical informatics.

The PhD curriculum for our trainees consists of formal instruction to provide the intellectual framework for conducting research.

Biomedical Informatics Core

• Informatics in Clinical Environments (MED 265): 1 Students are introduced to the basics of healthcare systems and clinical information needs through direct observation and classroom discussion. Students are introduced to medical language, disease processes, and health care practices to provide context prior to direct patient observation at primary, specialty, emergency, and inpatient sites in conjunction with clinical faculty affiliated with the training program. Students examine how clinicians use history-taking, physical examination and diagnostic testing to establish diagnoses and prognoses. Medical decision-making is introduced in the context of available informatics tools and clinical documentation and communication processes. Post-observation classroom discussions encourage students to think critically of the processes they observed and formulate hypotheses about how informatics solutions can modify the processes.
• Modeling Clinical Data and Knowledge for Computation (MED 267): This course describes existing methods for representing and communicating biomedical knowledge. The course describes existing health care standards and modeling principles required for implementing data standards, including biomedical ontologies, standardized terminologies, and knowledge resources.

1  Students with a clinical background will replace MED 265 with an additional course: Bioinformatics Applications to Human Disease (MED 263).

Bioinformatics Core

The core courses provide foundations in the biological basis of human health and disease and the statistical discovery of medical knowledge from biological experimentation. These classes are taken during the first year.

• Bioinformatics II (BENG 202) :  Introduction to methods for sequence analysis, applications to genome and proteome sequences, and protein structure and sequence-structure analysis.
• Principles of Biomedical Informatics (MED 264) : students are introduced to the fundamental principles of BMI and to the problems that define modern healthcare. The extent to which BMI can address healthcare problems is explored. Topics covered include structuring of data, computing with phenotypes, integration of molecular, image and other non-traditional data types into electronic medical records, clinical decision support systems, biomedical ontologies, data and communication standards, data aggregation, and knowledge discovery.
• Bioinformatics IV (MATH 283):  Analysis of modern genomic data, sequence analysis, gene expression/functional genomics analysis, and gene mapping/applied population genetics. The course focuses on statistical modeling and inference.

For the fourth core class, choose one of the following. In the event that a student completes two or more of these with suitable grades, one will count as core and the other(s) as electives.

• Algorithms in Computational Biology (CSE 280A): (Formerly CSE 206B) The course focuses on algorithmic aspects of modern bioinformatics and covers the following topics: computational gene hunting, sequencing, DNA arrays, sequence comparison, pattern discovery in DNA, genome rearrangements, molecular evolution, computational proteomics, and others. Prerequisites: CSE202 preferred or consent of instructor. 
• Algorithms for Biological Data Analysis (ECE 208): This course introduces a series of general algorithmic techniques but uses computational evolutionary biology as the context. The course motivates each algorithmic concept using a specific biological application related to evolution and focuses the discussion on specific types of (big) data available in modern biological studies. Note: The instructor and the BISB program are in the process of getting approval from the Graduate Council to introduce this as a course and to allow it as a core option. While we await approval, the course is offered under a temporary course number, ECE 286, by Prof. Siavash Mirarab, with the title "Algorithms for Biological Data Analysis." The course code ECE 286 may be used by other special topics courses as well, so be sure to enroll in the correct one.
• Genomics, Proteomics, and Network Biology (Bioinformatics III, BENG 203/CSE283): This is core in the BISB track. In the BMI track, it may be taken as the 4th core class or as an elective. Anotating genomes, characterizing functional genes, profiling, reconstructioning pathways.  Prerequisites: Pharm 201, BENG 202/CSE282, or consent of instructor. 

All students in years 1 and 2 must take both seminars in fall, winter, and spring quarters.

• Current Trends in Biomedical Informatics (MED 262): Weekly talks by researchers introduce students to current research topics within BMI. Speakers are drawn from academia, health care organizations, industry, and government.
• Bioinformatics Student Research Talks (BNFO 283) : Weekly presentations by Bioinformatics and Systems Biology students about Research Projects that are proposed or completed. Faculty mentors are present to contribute critiques and suggestions.

All students must take one of the two ethics courses by the end of second year. However, funding sources may require that it be taken first year, so we recommend taking it the first year.

• Scientific Ethics (SOMI 226): see below description
• Ethics in Scientific Research (BIOM 219): Overview of ethical issues in scientific research, conflicts of interest; national, statewide and campus issues and requirement; ethical issues in publications; authorship; retention of research records; tracing of research records; attribution; plagiarism; copyright considerations; primary, archival and meeting summary publications; ethical procedures and policies; NIH, NSF, California and UC San Diego; case studies and precedents in ethics.

Research and Teaching

During the academic year, all students must be enrolled in the appropriate research course for their level. Students typically do three rotations in year 1 (BNFO 298) and then do research units (BNFO 299) with their thesis advisor in years 2 and later. BNFO 299 units may be varied to meet the full-time enrollment requirement of 12 units per quarter in fall, winter, and spring.

• Teaching Assistantship (TA) (BNFO 500) :  Students will be a TA for two quarters during second or third year. To prepare for this teaching, students will receive training through the Center for Teaching Development at UCSD.
• Research Rotation (BNFO 298) : Taken each quarter during first year to help determine the thesis adviser.
• Graduate Research (BNFO 299): Independent work by graduate students engaged in research and writing theses. S/U grades only. May be taken for credit fifteen times.

Students must take 16 units of elective courses, including 8 units from the BMI series and 4 units from the CS series. The final 4 units can be taken from any series. The two BMI core courses MED 265 (or MED 263 for students with a clinical background) and MED 267 count as electives. Please check this  BISB curriculum page  for the list of all approved electives and elective series. 

Formal Progress to Degree

There are three formal evaluations that students must complete prior to being awarded a PhD degree: 

• Qualifying Examination:  This examination must be passed prior to the end of the student’s second year of study. The written portion of the exam consists of the student preparing an NIH or NSF-style research proposal. This proposal is then defended in an oral examination. Once the student passes the oral portion of the exam, the student is deemed to be qualified for advancing into PhD thesis research.
• Advancement to PhD Candidacy:  Upon completion of formal course requirements, each student is required to take a written and oral qualifying examination that admits the student to the candidacy of the PhD Program. The exam is administered by the dissertation committee, which consists of five faculty members.
• Final Examination:  All students defend their thesis in a final oral examination.

How to Apply

Application for admission to graduate studies is made directly through the Bioinformatics and Systems Biology website.

To be considered for the NLM fellowship, in addition to submitting your application and documentation to the degree program of your choice, please send the following to dbmi fellowship at ucsd dot edu:

• Personal Statement- explaining why you are a good candidate for the fellowship and what you hope to accomplish as an NLM trainee, the specific kind of research and topics you are interested in studying and what your goals are after completing the fellowship.
• A current and up to date CV; and
• In the body of your email please indicate which degree program you are applying to.

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Current Masters Students

• Requirements for the M.S. Degree

Qualified students can earn the MS degree within 3-5 quarters following receipt of the BS degree. Students enrolled in this program receive an advanced research experience by completing at least six contiguous quarters of biological research in one of the excellent research labs at UC San Diego. In addition, BS/MS students complete 12 units of graduate-level courses in Biology, Medicine, or other disciplines related to their thesis project. Students complete their degree requirements by writing and defending a Master's thesis.

Biology MS students should not rely on the graduate degree audit to track degree progress. Students may review the information below to confirm research and coursework requirements for the BS/MS program.

Consecutive Research

BS/MS students complete 6 consecutive quarters of research between the undergraduate and graduate programs.

• At least three complete, separate, and consecutive quarters of residency must be completed as a graduate student. These will commence immediately following the quarter in which the BS degree is awarded. Note, graduate students may not receive credit during the summer for research.
• All research must be completed within the same lab, with the same thesis advisor.
• Undergraduate research is measured through enrollment in BISP 199, BISP 196, or BISP 193. Undergraduate research used to satisfy degree requirements cannot be used to satisfy the BS/MS research requirement. 
• Graduate research is measured through enrollment in BGGN 271, in which the student must enroll during every quarter as an MS student.
• Research work will be credited toward the BS/MS program requirements only if it is completed while a student is officially enrolled at UC San Diego and has paid tuition for that quarter.

Enrollment and Coursework Requirements

MS students must complete at least 36 units of course work as a graduate student. Many students choose to complete more than the minimum required 36 units to help them achieve their goals.

Students need to be enrolled in 12 units each quarter (this includes both academic coursework and research units). There is no maximum unit load for a quarter.

Research Coursework

Students should enroll in both BGGN 271 and BGRD 200, with their thesis advisor as the instructor, for each quarter during the MS portion of this program. BGGN 271 is the graduate equivalent of BISP 19x. BGRD 200 accounts for the time spent discussing thesis research in the lab with a student's thesis advisor and lab colleagues. BGRD 200 is taken for 1 unit, while BGGN 271 can be taken for 4 to 12 units per quarter, reflecting the amount of time spent in the lab.

A total of 24 units of research coursework are needed between BISP 19x and BGGN 271, though BISP 19x research units do not apply toward 36 total Master's level units.

BGGN 299 and 297 are reserved for PhD students cannot be used to satisfy any of the 36 MS unit requirements.

Academic Coursework

Of the 36 graduate level units, at least 12 units must be in courses other than research (BGGN 271 and BGRD 200). Course selection should be determined in consultation with the MS thesis advisor, and all MS coursework must be approved by the thesis advisor when the student advances to candidacy in their final graduate quarter.

• Eligible course work must be graduate level (200-level or higher), but may include a maximum of four approved upper division units (100-199 level)
• Graduate level and upper division courses offered by related departments (BIOM, CHEM, MED, NEU SIO, etc.) may be used to satisfy this requirement.
• All course work must be taken for a letter grade, unless the course is only offered S/U or P/NP.
• Courses taken while an undergraduate student may not be repeated for credit during the graduate program.

Academic Coursework for students pursuing the Specialization in Biology Education Research (major code BI87)

Students pursuing the Specialization in Biology Education Research are required to complete 12 units of academic coursework, which must include BGGN 272: Learning Theories (4 units), completed with a letter grade. Of the remaining 8 units of academic coursework:

• A maximum of 4 units of upper division undergraduate coursework may satisfy this requirement.
• All courses satisfying this requirement must be completed for a letter grade, unless the course is only offered S/U or P/NP.

Recommended courses for students in this specialization include:

• EDS 102 Introduction to Qualitative Methods in Education Research (4 units)
• EDS 103 Introduction to Quantitative Analysis in Education Research (4 units)
• BGJC 215 Journal Club in Biology education research (1 unit)
• BGGN 202 Professional Development for Biologists (2 units)
• BGGN 211 Experimental Approaches & Methods in Modern Biology (4 units)
• BGGN 293 Scientific Writing in Biology (4 units)
• BGGN 295 Scientific Presentation in Biology (4 units)

Course selection should be determined in consultation with the MS thesis advisor, and all MS coursework must be approved by the thesis advisor when the student advances to candidacy in their final graduate quarter.

Courses Offered

For an overview of graduate courses offered in the current academic year, visit Tentative Course Offerings . For a list of courses open to MS students, visit Course Options for MS Students .

Graduate Residency, Minimum GPA, Fees

To meet the minimum requirements for a MS degree at UC San Diego, BS/MS students must complete at least 3 quarters of residency as a MS student. Summer cannot be used as a quarter of residency for MS students.

Additionally, BS/MS students must maintain a grade-point average of at least 3.000, both cumulatively and for each quarter of enrollment in the graduate program. If GPA falls below 3.000, the student may be dropped from the program.

Students should pay relevant fees during any quarter in which the student is using university resources (ex. working in lab or taking courses).

• Students must be enrolled full time while in the graduate program, unless approved for half time enrollment.
• To be eligible for half time , students must either be entering their 7th quarter of research or be requesting half time for health, family responsibilities, or occupation reasons. Students must meet with the BS/MS Coordinator prior to requesting half time status to confirm eligibility.
• Note: Students receiving financial support or employment at UC San Diego (such as an Instructional Assistant receiving a fee remission) must be enrolled in at least 12 units of graduate or upper division course work.

Any deviation from this plan, such as a break in enrollment for one or more quarters, may cause the student to be dropped from the program.

MS Thesis Committee

The MS thesis project completed by BS/MS students is evaluated by a MS Thesis Committee. MS students are responsible for establishing their MS Thesis Committee in consultation with their thesis advisor, and are expected to maintain communication with their committee throughout their MS program. Students officially nominate their MS committee when they advance to candidacy in their final quarter in the MS program.

The MS Thesis Committee:

• Must include at least three faculty members, including the thesis advisor who serves as the Committee Chair.
• Must include at least 2 tenure-track faculty from the School of Biological Sciences and no more than 1 adjunct faculty member.
• If the BS/MS thesis advisor is not a member of the School of Biological Sciences, or is an adjunct faculty member with the School of Biological Sciences, another member of the committee who is a tenure-track faculty member with the School of Biological Sciences must serve as Co-Chair.

Students are encouraged to form their Thesis Committee by the end of their first graduate quarter. Students are also encouraged to communicate regularly with their committee throughout the master's program to discuss the research project.

The MS Thesis Committee is responsible for approving a student's thesis and confirming that the student passed their thesis defense.

Master's thesis committees need at least three members, including the Chair (the student's thesis advisor/PI). Students are encouraged to create a committee that helps span the intellectual and technical breadth of their thesis project.

Committee member roles and eligible titles include:

• The student's faculty advisor serves as the MS Thesis Committee Chair.
• If a student's faculty advisor is not a tenure track faculty in the School of Biological Sciences, the thesis committee must have a Committee Co-Chair with a tenure track position in the School of Biological Sciences
• Students working in Biology labs may nominate a Committee Co-Chair if appropriate, however this is not required. Students in Biology labs should consult with their thesis advisor to determine if it is appropriate to nominate a Co-Chair.
• Students in the Education Specialization may have a co-chair with a Teaching Professor title (any rank)
• Faculty not serving as a Chair or Co-Chair on a thesis committee will serve as a Committee Member
• Students must have at least one committee member not serving as chair or co-chair
• All committee members must attend the thesis defense. Students are encouraged to limit membership on their thesis committee to avoid defense scheduling delays.
• Committee members must have one of the following faculty titles: Distinguished Professor, Professor Emeritus, Professor, Associate Professor, Assistant Professor, Teaching Professor (any rank)

Nominating the thesis committee

• Students confirm their committee chair and co-chair (or committee member, if appropriate) at the time they apply to the MS program.
• Students confirm their full committee, including the third committee member, when they advance to candidacy
• Students must nominate their MS committee with the BS/MS Coordinator to start the approval process.

Additional Information

General campus guidelines for appointing a Master's committee can be found on the Division of Graduate Education and Postdoctoral Affairs (GEPA) website . Note, all MS committees must meet the UC San Diego minimum requirements for a thesis committee as well as the School of Biological Sciences requirement that a thesis committee have at least 2 tenure-track Biology faculty.

Questions? Current UCSD students: Please submit your questions via the VAC . An advisor will respond in 1-3 business days. Drop-in Advising times are posted on the Advising Calendar .

• Course Options
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Biological Sciences, Division of

[ undergraduate program | courses | faculty ]

STUDENT AND INSTRUCTIONAL SERVICES OFFICE Pacific Hall, First Floor (858) 534-0557

All courses, faculty listings, and curricular and degree requirements described herein are subject to change or deletion without notice.

Contiguous Bachelor’s/Master’s Degree Program

A contiguous program leading to a bachelor of science and a master of science in biology is offered to those undergraduate students who are enrolled in any of the major programs offered by the Division of Biological Sciences at UC San Diego. Qualified students are able to obtain the MS within one year following receipt of the BS. Students interested in applying to this program should meet with the BS/MS adviser in the Biology Student and Instructional Services Office before the end of their junior year.

The program is open only to UC San Diego Biological Sciences undergraduates. The Division of Biological Sciences does not have financial aid available for students enrolled in this program. Students participating in the master’s program may apply to serve as an instructional assistant. For details, deadlines, and other information, please visit the biological sciences instructional assistants web page .

Eligibility and Enrollment

To be eligible, students must have completed the first two quarters of their junior year in residence at UC San Diego and must have an overall UC GPA of at least 3.0. Students’ major GPA should be at least 3.3. Students must demonstrate excellent performance in upper-division biology core courses during their undergraduate program to be eligible to enroll in biology graduate core courses.

It is the responsibility of the prospective BS/MS student to select a faculty member who would be willing to serve as the student’s adviser and in whose laboratory the student would complete at least twenty-four units of research over a two-year period. The units of research that must be completed during the student’s senior undergraduate year must be taken in addition to the requirements for the bachelor’s degree. These units will count toward the requirements for the master’s degree only. Students must complete six consecutive quarters of research to fulfill the research component of the program. Any deviation from this plan, such as a break in enrollment for one or more quarters, will be cause for the student to be dropped from the program.

Students who have been approved (by both the Division of Biological Sciences and the UC San Diego Office of Graduate Admissions) for the program must enroll in a Special Studies Course, BISP 193 or BISP 199 (senior year) and BGGN 271 (graduate year only), for each and every quarter of participation in the BS/MS program. Students can obtain the appropriate course code and departmental authorization at the Biology Student and Instructional Services Office.

Research work (BGGN 271) will be credited toward the BS/MS program requirements only if it is completed during the time a student is officially enrolled at UC San Diego and has paid tuition for that quarter.

Requirements for the Master of Science

• Completion of six consecutive quarters of research with the same mentor during the senior undergraduate year and the graduate period.
• Completion of at least thirty-six units of graduate course work (BGGN 200-level or higher, or approved [via petition] graduate courses offered by related departments at a similar level) during the graduate year. The course of study must be approved by the faculty adviser.
• Twelve of the thirty-six units must be in courses other than BGGN 271. (BGGN 297 and BGGN 299 may not be used to satisfy this requirement.)
• Maintenance of a grade point average (both overall and in the major) of at least 3.0 for all course work, both cumulatively and for each quarter of enrollment in the BS/MS program. If the student’s GPA falls below 3.0 (for either overall or in the major), he or she will be automatically dropped from the program.
• Completion of a thesis, with an oral presentation to, and approval of, a three-member thesis committee. The research adviser and thesis committee chair must be a ladder rank or adjunct faculty member in the Division of Biological Sciences, except in cases where the research project has an educational theme (initiated via enrollment in BISP 193), where the adviser and committee chair may be a teaching professor in the Division of Biological Sciences who has been approved for this role by the Academic Senate. The thesis committee must contain at least two Academic Senate faculty from the Division of Biological Sciences; no more than one adjunct faculty can serve on the committee. If an adjunct faculty serves as chair of the thesis committee, one of the biology faculty members must serve as cochair.
• At least three complete, separate, and consecutive quarters of residency as a graduate student that will commence the quarter immediately following the quarter in which the BS is awarded. (Note: The summer session is not considered an official quarter during the graduate year.)
• Students who have been approved for the BS/MS program must provide the Office of Graduate Admissions with a copy of their official UC San Diego transcripts with the BS posted, prior to the commencement of the graduate year in the program.

The Doctoral Program

Graduate studies for a PhD in the Division of Biological Sciences in affiliation with the Salk Institute for Biological Studies are oriented mainly toward the development of the capacity for independent research and for teaching in the biological sciences.

The requirements for entrance to graduate study in the Division of Biological Sciences are flexible, but a strong background in mathematics, chemistry, and physics is recommended.

Formal course work and opportunities for dissertation research include most basic areas of experimental biology, with emphasis in the general areas of biochemistry, biophysics, cancer biology, cell biology, conservation, developmental biology, ecology, behavior, and evolution, genetics, immunology, molecular biology, neurobiology, plant molecular biology, plant systems biology, quantitative biology, signal transduction, systems biology, and virology.

During the first year of graduate study, each student undertakes a research project in the laboratory of each of four to six different faculty members and is expected to spend a major portion of his or her academic time on this project. The laboratories are selected by the student in consultation with the first-year adviser to provide a broad view of the research interests of the division. The student is also expected to enroll in the first-year graduate biology sequence, which includes a “boot camp” that helps develop fundamental lab skills in biology, as well as courses on bioinformatics, biostatistics, and methods and logic in biological sciences. Students are also required to complete course and practicum requirements as part of the Graduate Instructional Apprentice program. Development of teaching skills is a key goal for students in our doctoral program. Students will serve three times as an instructional assistant (IA) and enroll in a course on teaching and mentoring. This course has an in-class component led by a faculty member with expertise in evidence-based teaching methods, and an apprentice-teaching component supervised by a biology course instructor. Doctoral students must receive a satisfactory evaluation from all instructors in whose courses they serve as IAs. This part of our program aims to prepare doctoral students for future careers that involve teaching and mentoring.

A program of further study, including seminars and courses appropriate to a student’s background and interests, is arranged through consultation between the student and the faculty. Much reliance is placed on informal instruction through early and close association of the student with the faculty and research staff, and through regular seminars. After becoming familiar with the research activities of the faculty through the laboratory rotation program, the student begins work on a thesis research problem of his or her choice no later than the end of the first year. The student is free to choose, for the thesis adviser, a regular member of the UC San Diego faculty or an adjunct member of the Division of Biological Sciences faculty. The student is required to have completed a two-part examination in order to be admitted to candidacy for the PhD. The purpose of the examinations is for the student to demonstrate competence in the field of major interest and in related fields of biology. The major remaining requirement for the PhD is the satisfactory completion of a dissertation consisting of original research carried out under the guidance of a faculty member.

Close collaboration with members of the Department of Chemistry and Biochemistry is a vital and stimulating aspect of the biology program. Additional strength and breadth in biology are gained by collaborating with the Department of Marine Biology of the Scripps Institution of Oceanography, with The Scripps Research Institute, and with the Salk Institute for Biological Studies.

Divisional PhD Time Limit Policies

Students must be advanced to candidacy by the end of four years. Total university support cannot exceed seven years. Total registered time at UC San Diego cannot exceed seven years.

Joint Doctoral Program with San Diego State University

The Division of Biological Sciences at UC San Diego participates in a joint graduate program with the Department of Biology at San Diego State University, primarily in the areas of cell and molecular biology, and leading to the PhD in biology. Graduate student participants in the joint doctoral program are required to spend one year enrolled at UC San Diego.

Information regarding admission is found in the current edition of the San Diego State University Graduate Bulletin.

Specialization in Anthropogeny

http://carta.anthropogeny.org/training/specialization-track

A transdisciplinary graduate specialization in anthropogeny is available for doctoral students in the Division of Biological Sciences. The aim of the specialization is to provide graduate students the opportunity to specialize their research and education in addressing the origins of the human phenomenon. The student’s research will be related to one of the oldest questions known to humankind, namely, the origins of humans and humanity. This specialization is not a stand-alone program, but will provide graduate students the opportunity to interact and communicate with peers in radically different disciplines throughout the duration of their PhD projects. Such communication across disciplines from the outset is key to fostering a capacity for interdisciplinary language skills and conceptual flexibility.

Admission to the Specialization

Students are admitted into the Division of Biological Sciences doctoral program. During the early stages of their program, currently enrolled biology students with an interest in human origins are eligible to apply for admission to the specialization in anthropogeny. Selected applicants will have the opportunity to enroll in the specialization.

Specialization Requirements

Students pursuing this specialization must satisfy the requirements of both the biology doctoral program and the specialization in anthropogeny. For the anthropogeny specialization, students will be required to take a series of courses and participate in research rounds over four years of study. It is advised that students begin their course work in their second year.

• Course work: Introduction to Anthropogeny (BIOM 225) and Advanced Anthropogeny (BIOM 229) are each taken once, in the winter and spring of the students’ second year. Current Topics in Anthropogeny (BIOM 218) is to be taken for six quarters (twice per academic year).
• Research Rounds: Monthly seminars during which all participating students talk about their respective research.

Degree Requirements (Qualifying Examination, Dissertation)

Biological sciences students in the anthropogeny specialization must meet the departmental requirement for advancement to candidacy. In addition, students must meet internal deadlines, mentoring provisions, and proposal standards of the anthropogeny specialization track.

PhD students must complete a dissertation, which meets all requirements of the biological sciences program. In addition, it is expected that the PhD dissertation is broadly related to human origins and will be interdisciplinary in nature.

Time Limits

Students admitted to the specialization in anthropogeny must meet the time limit requirements as all other doctoral students in the Division of Biological Sciences. It is expected that students will retain the same time to degree as students not pursuing this specialization. Additional course load consists only of two regular courses (two quarters, twenty lectures each). The third proposed course takes place only three times a year, from Friday noon to Saturday evening.

Specialization in Multiscale Biology

http://interfaces.ucsd.edu/

The UC San Diego campus offers a PhD specialization in Multiscale Biology available to doctoral candidates in participating programs spanning four divisions: Biological Sciences, Physical Sciences, Jacobs School of Engineering, and Health Sciences at UC San Diego.

The PhD specialization is designed to allow students to obtain standard basic training in their chosen field within the biological sciences, physical sciences, engineering, and health sciences with training in integrative and quantitative analysis across multiple scales of biological organization from molecule to organism in health and disease into their graduate studies. It trains a new cadre of PhD scientists and provides a unique interdisciplinary education at the interfaces between the biological, medical, physical, and engineering sciences.

The specific objectives of this program are

• Focused collaboration across nine graduate degree programs at UC San Diego to train a new generation of cross-disciplinary scientists
• State-of-the-art interdisciplinary training through a new technology-centered hands-on graduate laboratory course curriculum
• Novel emphasis on research aimed at integrative and quantitative analysis across multiple scales of biological organization from molecule to organism in health and disease

Prospective students must apply and be admitted into the PhD program in biological sciences described previously. (For more information, see the Biological Sciences Graduate Program and/or the Interfaces Graduate Training Program .)

Specialization in Quantitative Biology

A specialization in Quantitative Biology (Q-Bio) spanning four divisions—Biological Sciences, Physical Sciences, Jacobs School of Engineering, and Health Sciences—is available to doctoral candidates in the Division of Biological Sciences. This PhD specialization is designed to train students to develop and apply quantitative theoretical and experimental approaches to studying fundamental principles of living systems. The core of this specialization comprises one year of theory courses and one year of lab courses.

Admission to the Specialization and Course Requirements

Prospective students should apply to and are admitted into the Division of Biological Sciences doctoral program. Admitted students must complete the core sequence within Biological Sciences. In addition, they must complete two additional Q-Bio courses and a one-year laboratory course sequence during their first two years in the specialization. Students will complete laboratory rotations during their first year. For more information students should contact the Biological Sciences’ Graduate Student and Instructional Services Office.

Specialization in Interdisciplinary Environmental Research

A graduate specialization in Interdisciplinary Environmental Research (PIER) is available for select doctoral students in biology. PIER students seek solutions to today’s environmental challenges.

The PhD specialization is designed to allow students to obtain standard training in their chosen field and an opportunity to interact with peers in different disciplines throughout the duration of their doctoral projects. Such communication across disciplines is key to fostering a capacity for interdisciplinary “language” skills and conceptual flexibility.

• Complete all course work, dissertation, and other requirements of the biological science doctorate  
• 16-unit interdisciplinary boot camp (summer, SIO 295S–295LS)
• 8 units from a secondary field (outside the home department)
• 6 units (3 quarters) Interdisciplinary Environmental Research Forum (SIO 296)
• At least one chapter of the dissertation will be broadly related to environmental research and will be interdisciplinary in nature.

Application Requirements

We advise students to begin PIER in their second year upon completion of core biology course requirements.

The following items should be combined into a single PDF document and submitted to [email protected] .

• Student’s CV
• Half-page abstract of proposed thesis work
• Up to one-page statement of student’s interest in interdisciplinary environmental research including career goals
• Nomination letter from adviser acknowledging student’s academic ability and interdisciplinary environmental interest. The letter must include a commitment for summer stipend support.

Students are admitted into the biological sciences doctoral program. Admission to PIER is a competitive process with six to eight students granted admission each year from across ten participating UC San Diego departments. Selected applicants will have the opportunity to enroll in the specialization.

PIER Fellowships

When funding is available, all applicants will be considered for one year of PIER Fellowship support. 

Course Descriptions

See here for a list of projected course offerings for 2023-24. For departments/classes that have not announced projected schedules, contact the instructor(s) or department for information.

All Core and Elective courses for the degree must be taken for a letter grade. Students must obtain a “B” or better in courses taken for the degree. If you receive a “B-” or lower in a Core or Elective class, or you take it on S/U grading, it does not fulfill your requirements. Please see the Grades FAQ if you have any grades of “B-” or lower or “U”.

Core Requirements

Core classes must be completed in the first two years, and usually are completed the first year.

Each student in the Bioinformatics and Systems Biology (BISB) track must take four core courses:

Bioinformatics II (BENG 202/CSE 282). Introduction to Bioinformatics Algorithms (4 units)

(Formerly BENG 202/CSE 257A.) Introduction to methods for sequence analysis. Applications to genome and proteome sequences. Protein structure, sequence-structure analysis. Prerequisite: Pharm 201 or consent of instructor. (W)

Bioinformatics III (BENG 203/CSE 283). Genomics, Proteomics, and Network Biology (4 units)

Annotating genomes, characterizing functional genes, profiling, reconstructing pathways. Prerequisites: Pharm 201, BENG 202/CSE 282, or consent of instructor. (S)

Bioinformatics IV (MATH 283). Statistical Methods in Bioinformatics (4 units)

This course will cover material related to the analysis of modern genomic data; sequence analysis, gene expression/functional genomics analysis, and gene mapping/applied population genetics. The course will focus on statistical modeling and inference issues and not on database mining techniques. Prerequisites: one year of calculus, one statistics course or consent of instructor.

• One class selected from the “Fourth Core Class” options below (except BENG 203/CSE 283).

Each student in the Biomedical Informatics (BMI) track must take four core courses:

MED 264. Principles of Biomedical Informatics (4 units)

Students are introduced to the fundamental principles of BMI and to the problems that define modern healthcare. The extent to which BMI can address healthcare problems is explored. Topics covered include structuring of data, computing with phenotypes, integration of molecular, image and other non-traditional data types into electronic medical records, clinical decision support systems, biomedical ontologies, data and communication standards, data aggregation, and knowledge discovery. (F)

• One class selected from the “Fourth Core Class” options below.

For the fourth core class, choose one of the following. In the event that a student completes two or more of these with suitable grades, one will count as core and the other(s) as electives. (If an additional fourth core class is not on the list of electives, it can count towards the required 16 units of electives, but not towards an elective field requirement like CS or BIO.) Some options may not be offered every year; choose from options available by your deadlines.

CSE 280A. Algorithms in Computational Biology (4 units)

(Formerly CSE 206B.) The course focuses on algorithmic aspects of modern bioinformatics and covers the following topics: computational gene hunting, sequencing, DNA arrays, sequence comparison, pattern discovery in DNA, genome rearrangements, molecular evolution, computational proteomics, and others. Prerequisites: CSE 202 preferred or consent of instructor.

CSE 284. Personal Genomics for Bioinformaticians (4 units)

This course provides an introduction to bioinformatics techniques for analyzing and interpreting human genomes. Topics covered include an introduction to medical and population genetics, ancestry, finding and interpreting disease-causing variants, genome-wide association studies, genetic risk prediction, analyzing next-generation sequencing data, how to scale current genomics techniques to analyze hundreds of thousands of genomes, and the social impact of the personal genomics revolution. Programming experience, familiarity with the UNIX command line, and a basic course in probability and statistics are strongly recommended. Students may not receive credit for CSE 284 and CSE 291 (E00) taught winter 2017 with the same subtitle. Prerequisites: graduate standing.

ECE 208. Computational Evolutionary Biology (4 units)

Evolutionary biology (e.g., the study of the tree of life) uses computational methods from statistics and machine learning. We cover methods of broad use in many fields and apply them to biology, focusing on scalability to big genomic data. Topics include dynamic programming, continuous time Markov models, hidden Markov models, statistical inference of phylogenies, sequence alignment, uncertainty (e.g., bootstrapping), and heterogeneity (e.g., phylogenetic mixture models). Prerequisites: graduate standing.

BNFO 286. Network Biology and Biomedicine (4 units)

(Cross-listed with MED 283.) Networks are pervasive in molecular biology and medicine. This course introduces biomolecular networks and their major analysis techniques and roles in biomedical research, including pathway-based genetic analysis. Recommended familiarity with bioinformatics programming; course examples are taught in Python. Prerequisites: Genetics (BICD 100, BGGN 223, or BIOM 252) and graduate-level statistics (MED 268, MATH 283, MATH 281A, MATH 281C, FMPH 221, or FMPH 222). Prerequisites may be waived with consent of instructor.

Bioinformatics III (BENG 203/CSE 283). Genomics, Proteomics, and Network Biology (4 units) – This is core in the BISB track. In the BMI track, it may be taken as the 4th core class or as an elective.

All students in years 1-2 must take the Colloquium for their track in fall, winter, and spring quarters: BNFO 281 for the BISB track, or MED 262 for the BMI track.

BNFO 281. Seminar in Bioinformatics and Systems Biology (1 unit)

Weekly seminars by faculty and visiting bioinformaticists presenting their research. S/U grades only. May be taken for credit nine times.

MED 262. Current Trends in Biomedical Informatics (1 unit)

Weekly talks by researchers introduce students to current research topics within BMI. Speakers are drawn from academia, health care organizations, industry, and government. (F,W,S)

All students in years 1-2 must take the Student Research Talks in fall, winter, and spring quarters.

BNFO 283. Bioinformatics Student Research Talks (1 unit)

Weekly presentations by bioinformatics and systems biology students about research projects that are proposed or completed. Faculty mentors are present to contribute critiques and suggestions. S/U grades only. May be taken for credit nine times. Prerequisites: bioinformatics and systems biology program graduate students only.

All students must take the ethics course BNFO 294 (previously SOMI 226 or BIOM 219) by the end of the second year. However, funding sources may require that it be taken the first year, so we recommend taking it the first year; in particular, all students on NIH training grants or other NIH funding are required to take ethics in their first year.

Special registration procedure: Students must register for the ethics course both via WebReg as well as via the “Scientific Ethics” registration form on ethics.ucsd.edu; please do both of these steps promptly when the courses open up, as they may fill quickly. The course is taken by many UCSD employees (not just students), so the Ethics Program uses its own registration form. Registration on WebReg is necessary for students to receive course credit. To take it in the summer, register on ethics.ucsd.edu, and give the “certificate of completion” to the BISB graduate coordinator, in lieu of BNFO 294 credit on your transcript.

BNFO 294. Scientific Ethics (1 unit)

Lectures, readings, and discussions about the responsible conduct and reporting of research, working with others in science, and social responsibilities; the course is designed as an option for meeting federal regulations for such training. S/U grades only. Prerequisites: Bioinformatics and Systems Biology graduate students.

Students must also take the Scientific Ethics Refresher Course every four years thereafter; e.g., students who take BNFO 294 in their first year should take the Refresher in years 5 and 9 (if still here). The Refresher course does not have a course number and will not appear on your transcript. Register for it on ethics.ucsd.edu only (not WebReg). Afterwards, give the “certificate of completion” to both the BISB Graduate Coordinator and your advisor (it may be needed for their grant report).

Research Requirements

During the academic year, all students must be enrolled in the appropriate research course for their level. Students typically do three rotations in year 1 (BNFO 298) and then do research units (BNFO 299) with their thesis advisor in years 2 and later. BNFO 299 units may be varied to meet the full-time enrollment requirement of 12 units per quarter in fall, winter, and spring. During the summer, students are expected to do research as well, but should not enroll in BNFO 298 or BNFO 299. During all quarters and the summer, students are responsible for satisfying program requirements including proposals, reports, presentations, committee meetings, notifying the graduate coordinator when joining/changing labs, etc.; the only difference is that students do not enroll in BNFO 298 or BNFO 299 in the summer. In addition, each student will make periodic research presentations to the graduate program students/faculty. Students will also discuss their progress at the annual program meeting to be held each year.

BNFO 298. Research Rotation (4 units)

Laboratory research of special topics under the direction of a program faculty member. The purpose is to train students in specific research methodologies and identify a laboratory in which to pursue doctoral dissertation research. Three quarters are required for PhD candidates. May be taken for credit up to six times. Prerequisites: bioinformatics graduate students and consent of instructor and program.

BNFO 299. Graduate Research (1–12 units)

Independent work by graduate students engaged in research and writing theses. S/U grades only. May be taken for credit fifteen times. Prerequisites: bioinformatics and systems biology graduate students and consent of instructor.

Teaching Requirements

All students must serve as a teaching assistant (TA) for at least two quarters. Please contact the BISB graduate coordinator by email in advance of each teaching assistantship to complete required paperwork and other administrative arrangements.

Students should enroll in BNFO 500 (Teaching Experience) or an equivalent course code in another department (BENG 501, BGGN 500, CHEM 500, CSE 500, MATH 500, etc.), during each quarter in which they are a teaching assistant. For summer teaching assistantships, please contact the BISB graduate coordinator to record it in lieu of BNFO 500 credit.

A typical teaching assistantship is 110 hours/quarter (25% load, 2 units of BNFO 500); however, this varies by class. 220 hours/quarter is a 50% load, 4 units.

Students are strongly encouraged to do only 25% teaching assistantships, due to the impact on time available for coursework and research. If you are considering a 50% position, please check if it can be split into two 25% positions. Please submit a petition to the BISB Curriculum Committee for any position with a load above 25%.

BNFO 500. Teaching Assistantship (2–4 units)

Teaching experience in an appropriate bioinformatics undergraduate or graduate course under direction of the faculty member in charge of the course. Each PhD candidate must complete two academic quarters of experience for S/U grade only. May be taken for credit four times. Prerequisites: graduate standing and consent of instructor (department stamp). (F,W,S)

Program Electives

Each student must select 16 units of Elective Courses from the Elective Fields (BIO, CS, SB, BMI, QBIO) delineated below, according to the rules for their track. If a class is available both as an elective and as a core class, it may only be used to satisfy one of those requirements, not both. Some options may not be offered every year; choose from options available by your deadlines.

Electives are started in the first year and usually completed within the first two years. However, the Second Year Qualifying Examination may be taken even if electives are not completed.

It is the general policy of the program to be as adaptable as possible to the needs of the individual student: the curriculum committee is receptive to students petitioning to satisfy an Elective requirement by taking a course not listed among the Electives (see the Curriculum Petitions FAQ ).

BISB track: Each student must take at least 4 units from the CS series and 4 units from the BIO series. For example, a student interested in Systems Biology could take one 4 unit class from the CS series, one from the BIO series, one from SB-1, and one from SB-2.

BMI track: Each student must take at least 4 units from the CS series and 8 units from the BMI series. BMI students should take MED 265 and 267 as electives to fulfill DBMI's trainee requirements. (Students with a clinical background should replace MED 265 by MED 263.) DBMI trainees should see the DBMI website for information about additional requirements and other DBMI courses.

Please consult your advisor about which courses are required depending on status related to funding, graduate program, etc.

Elective BIO-1: Biochemistry

Beng 230a. biochemistry (4 units).

A graduate course in biochemistry especially tailored to the requirements and background of bioengineering graduate students. It will cover the important macro- and small molecules in cells that are the major constituents, or that function as signaling molecules or molecular machineries. The structures, pathways, interactions, methodologies, and molecular designs using recombinant DNA technology will be covered. Prerequisites: restricted to bioengineering graduate students with major code BE75. (F)

CHEM 209. Macromolecular Recognition (4 units)

Structures and functions of nucleic acids, folding and catalysis of nucleic acids, motifs and domains of proteins, principles of protein-protein interactions, chemistry of protein/DNA and protein/RNA interfaces, conformational changes in macromolecular recognition. Prerequisites: biochemistry background and graduate standing, or approval of instructor.

CHEM 213A. Structure of Biomolecules and Biomolecular Assemblies (4 units)

A discussion of structures of nucleic acids and proteins and their larger assemblies. The theoretical basis for nucleic acid and protein structure, as well as methods of structure determination including X-ray crystallography, cryoEM, and computational modeling approaches will be covered. Letter grades only. Prerequisites: graduate standing.

CHEM 213B. Biophysical Chemistry of Macromolecules (4 units)

Renumbered from CHEM 213. A discussion of the physical principles governing biomolecular structure and function. Experimental and theoretical approaches to understand protein dynamics, enzyme kinetics, and mechanisms will be covered. Students may only receive credit for one of the following: CHEM 213 or 213B. May be co-scheduled with CHEM 113.

Note: Previously, CHEM 213 was a program elective. The syllabus has been split and expanded into two quarters, CHEM 213A and 213B. You may take either one, or may take both in either order. The courses will be offered in alternate years.

CHEM 216. Chemical Biology (4 units)

A discussion of current topics in chemical biology including mechanistic aspects of enzymes and cofactors, use of modified enzymes to alter biochemical pathways, chemical intervention in cellular processes, and natural product discovery. Prerequisites: graduate standing or consent of instructor. (May not be offered every year.)

Elective BIO-2: Molecular Genetics

Bicd 100. genetics (4 units).

An introduction to the principles of heredity emphasizing diploid organisms. Topics include Mendelian inheritance and deviations from classical Mendelian ratios, pedigree analysis, gene interactions, gene mutation, linkage and gene mapping, reverse genetics, population genetics, and quantitative genetics. Students may receive credit for one of the following: BICD 100 or BICD 100R. Prerequisites: BILD 1 and BILD 3.

BGGN 206A. Concepts of Reasoning and Experimentation (CORE) I (4 units) – Request authorization from Biology to enroll using EAsy .

This course focuses on key concepts and the methods and logic used to ask and answer challenging biological questions. Course work will be organized around fundamental topics in molecular and cell biology and focus on problem solving, research articles, and/or research seminars to examine best practices in making reasoned scientific arguments and using logical experimental design to tackle biological problems, particularly at the molecular and cellular level. Enrollment restricted to the following major codes: BI77 and BI78.

BGGN 220. Graduate Molecular Biology (4 units)

Provides a broad, advanced-level coverage of modern molecular biology for graduate students. Topics include gene structure and regulation, chromatin structure, mechanisms of transcription, RNA processing, translation, and turnover. The format includes lectures and discussion of selected papers. Letter grades only.

BGGN 223. Graduate Genetics (4 units)

Advanced coverage of classical and cutting-edge genetic technologies in a wide variety of organisms—bacteria, plants, insects, worms, fish, and mammals. The power of genetic approaches to provide fundamental insights into important questions in development, physiology, behavior, medicine, and evolution. Course format centered on discussion of research papers with genetic analysis at their core. Emphasis on exploring essential genetic concepts, principles, and mechanisms throughout biology. Letter grades only.

Elective BIO-3: Cell Biology

Bicd 110. cell biology (4 units).

The structure and function of cells and cell organelles, cell growth and division, motility, cell differentiation and specialization. Prerequisites: BIBC 100 or BIBC 102 or CHEM 114A or CHEM 114B.

BICD 130. Embryos, Genes, and Development (4 units)

Developmental biology of animals at the tissue, cellular, and molecular levels. Basic processes of embryogenesis in a variety of invertebrate and vertebrate organisms. Cellular and molecular mechanisms that underlie cell fate determination and cell differentiation. More advanced topics such as pattern formation and sex determination are discussed. Open to upper-division students only. Recommended preparation: BICD 110 and BIMM 100. Prerequisites: upper-division standing; BICD 100 or BICD 100R and BIBC 100 or BIBC 102 or CHEM 114A or CHEM 114B.

BGGN 222. Graduate Cell Biology (4 units)

Coverage of modern cell biology. Topics will be chosen from the following: the structure and function of membranes; endocytosis; protein targeting; intracellular organelles, including the nucleus, ER, Golgi; the cytoskeleton and molecular motors; mitosis and cell division; autophagy; cell death; cell signaling; cell-cell interactions. The course will include discussions on molecular approaches to cell biology as well as dissecting interconnections between cell biology and disease. Letter grades only.

CHEM 221 / BGGN 230. Signal Transduction (4 units)

(Cross-listed with BGGN 230.) The aim of this course is to develop an appreciation for a variety of topics in signal transduction. We will discuss several historical developments while the focus will be on current issues. Both experimental approaches and results will be included in our discussions. Topics may vary from year to year. Prerequisites: biochemistry and molecular biology. (May not be offered every year.)

Elective CS-1: Algorithms

Cse 101. design and analysis of algorithms (4 units).

Design and analysis of efficient algorithms with emphasis of nonnumerical algorithms such as sorting, searching, pattern matching, and graph and network algorithms. Measuring complexity of algorithms, time and storage. NP-complete problems. Prerequisites: CSE 21 or MATH 154 or MATH 158 or MATH 184 or MATH 188 and CSE 12 or DSC 30; restricted to undergraduates. Graduate students will be allowed as space permits.

CSE 200. Computability and Complexity (4 units)

Computability review, including halting problem, decidable sets, r.e. sets, many-one reductions; TIME(t(n)), SPACE(s(n)) and general relations between these classes; L, P, PSPACE, NP; NP—completeness; hierarchy theorems; RP, BPP. Prerequisites: CSE 105 or equivalent.

CSE 202. Algorithm Design and Analysis (4 units)

The basic techniques for the design and analysis of algorithms. Divide-and-conquer, dynamic programming, data structures, graph search, algebraic problems, randomized algorithms, lower bounds, probabilistic analysis, parallel algorithms. Prerequisites: CSE 101 or equivalent.

MATH 261A. Probabilistic Combinatorics and Algorithms (4 units)

Introduction to the probabilistic method. Combinatorial applications of the linearity of expectation, second moment method, Markov, Chebyschev, and Azuma inequalities, and the local limit lemma. Introduction to the theory of random graphs. Prerequisites: graduate standing or consent of instructor.

Elective CS-2: Machine Learning and Data Mining

Bnfo 285. statistical learning in bioinformatics (4 units).

(Cross-listed with ECE 204 and BENG 285.) A hallmark of bioinformatics is the computational analysis of complex data. The combination of statistics and algorithms produce statistical learning methods that automate the analysis of complex data. Such machine learning methods are widely used in systems biology and bioinformatics. This course provides an introduction to statistical learning and assumes familiarity with key statistical methods. Letter grades only. Students may not receive credit for BNFO 285 and ECE 204 and BENG 285.  Prerequisites: MATH 283 or ECE 271A or ECE 271B.

CSE 250A. Principles of Artificial Intelligence: Probabilistic Reasoning and Learning (4 units)

Methods based on probability theory for reasoning and learning under uncertainty. Content may include directed and undirected probabilistic graphical models, exact and approximate inference, latent variables, expectation-maximization, hidden Markov models, Markov decision processes, applications to vision, robotics, speech, and/or text. Recommended preparation: CSE 103 or similar course. Prerequisites: graduate standing in CSE or consent of instructor.

CSE 251A. Principles of Machine Learning: Learning Algorithms (4 units)

(Formerly CSE 250B.) Algorithms for supervised and unsupervised learning from data. Content may include maximum likelihood; log-linear models, including logistic regression and conditional random fields; nearest neighbor methods; kernel methods; decision trees; ensemble methods; optimization algorithms; topic models; neural networks; and backpropagation. Renumbered from CSE 250B. Students may not receive credit for CSE 251A and CSE 250B. Recommended preparation: CSE 103 or similar course. Prerequisites: graduate standing or consent of instructor.

CSE 251B. Principles of Machine Learning: Neural Networks for Pattern Recognition (4 units)

(Formerly CSE 253.) This course covers Hopfield networks, application to optimization problems layered perceptrons, recurrent networks, and unsupervised learning. Programming exercises explore model behavior with a final project or exam on a cognitive science, artificial intelligence, or optimization problem of the student’s choice. Renumbered from CSE 253. Students may not receive credit for CSE 251B and CSE 253. Recommended preparation: Knowledge of C. Prerequisites: graduate standing.

CSE 255. Data Mining and Predictive Analytics (4 units)

Learning methods for applications. Content may include data preparation, regression and classification algorithms, support vector machines, random forests, class imbalance, overfitting, decision theory, recommender systems and collaborative filtering, text mining, analyzing social networks and social media, protecting privacy, A/B testing. Recommended preparation: CSE 103 or similar. Prerequisites: graduate standing or consent of instructor.

CSE 258. Recommender Systems and Web Mining (4 units)

Current methods for data mining and predictive analytics. Emphasis is on studying real-world data sets, building working systems, and putting current ideas from machine learning research into practice. Recommended preparation: No previous background in machine learning is required, but students should be comfortable with programming (all example code will be in Python), and with basic optimization and linear algebra. Prerequisites: graduate standing.

Elective CS-3: Mathematics and Statistics

Ece 271a. statistical learning i (4 units).

Bayesian decision theory; parameter estimation; maximum likelihood; the bias-variance trade-off; Bayesian estimation; the predictive distribution; conjugate and noninformative priors; dimensionality and dimensionality reduction; principal component analysis; Fisher’s linear discriminant analysis; density estimation; parametric vs. kernel-based methods; expectation-maximization; applications. Recommended preparation: ECE 109. Prerequisites: graduate standing.

MATH 274. Numerical Methods for Physical Modeling (4 units)

(Conjoined with MATH 174.) Floating point arithmetic, direct and iterative solution of linear equations, iterative solution of nonlinear equations, optimization, approximation theory, interpolation, quadrature, numerical methods for initial and boundary value problems in ordinary differential equations. Students may not receive credit for both MATH 174 and PHYS 105, AMES 153 or 154. (Students may not receive credit for MATH 174 if MATH 170A, B, or C has already been taken.) Graduate students will complete an additional assignment/exam. Prerequisites: MATH 20D or 21D, and either MATH 20F or MATH 31AH, or consent of instructor.

MATH 280A. Probability Theory I (4 units)

This is the first course in a three-course sequence in probability theory. Topics covered in the sequence include the measure-theoretic foundations of probability theory, independence, the Law of Large Numbers, convergence in distribution, the Central Limit Theorem, conditional expectation, martingales, Markov processes, and Brownian motion. Recommended preparation: completion of real analysis equivalent to MATH 140A-B strongly recommended. Prerequisites: graduate standing.

MATH 281A. Mathematical Statistics (4 units)

Statistical models, sufficiency, efficiency, optimal estimation, least squares and maximum likelihood, large sample theory. Prerequisites: advanced calculus and basic probability theory or consent of instructor.

MATH 281B. Mathematical Statistics (4 units)

Hypothesis testing and confidence intervals, one-sample and two-sample problems. Bayes theory, statistical decision theory, linear models and regression. Prerequisites: advanced calculus and basic probability theory or consent of instructor.

MATH 281C. Mathematical Statistics (4 units)

Nonparametrics: tests, regression, density estimation, bootstrap and jackknife. Introduction to statistical computing using S plus. Prerequisites: advanced calculus and basic probability theory or consent of instructor.

MATH 282A. Applied Statistics I (4 units)

General theory of linear models with applications to regression analysis. Ordinary and generalized least squares estimators and their properties. Hypothesis testing, including analysis of variance, and confidence intervals. Completion of courses in linear algebra and basic statistics are recommended prior to enrollment. Prerequisites: graduate standing or consent of instructor. (S/U grades permitted.)

MATH 282B. Applied Statistics II (4 units)

Diagnostics, outlier detection, robust regression. Variable selection, ridge regression, the lasso. Generalized linear models, including logistic regression. Data analysis using the statistical software R. Students who have not taken MATH 282A may enroll with consent of instructor. Prerequisites: MATH 282A or consent of instructor. (S/U grades permitted.)

MATH 284. Lifetime Data Analysis (4 units)

Survival analysis is an important tool in many areas of applications including biomedicine, economics, engineering. It deals with the analysis of time to events data with censoring. This course discusses the concepts and theories associated with survival data and censoring, comparing survival distributions, proportional hazards regression, nonparametric tests, competing risk models, and frailty models. The emphasis is on semiparametric inference, and material is drawn from recent literature. Students who have not completed listed prerequisites may enroll with consent of instructor. Prerequisites: MATH 282A. Students who have not completed listed prerequisite may enroll with consent of instructor.

PHYS 210A. Equilibrium Statistical Mechanics (5 units)

Statistical ensembles: microcanonical, canonical, and grand canonical formulations; principle of maximum entropy. Thermodynamics: thermodynamic potentials, phase equilibria, entropy of mixing. Quantum statistics: photon statistics; ideal Bose and Fermi gases. Interacting systems: Ising model, liquids and plasmas. Phase transitions: van der Waals system, mean field theory, Landau theory, global symmetries, fluctuations. Prerequisites: PHYS 200A, 212A-B.

PHYS 210B. Nonequilibrium Statistical Mechanics (4 units)

Transport phenomena; kinetic theory and the Chapman-Enskog method; hydrodynamic theory; nonlinear effects and the mode coupling method. Stochastic processes; Langevin and Fokker-Planck equation; fluctuation-dissipation relation; multiplicative processes; dynamic field theory; Martin-Siggia-Rose formalism; dynamical scaling theory. Prerequisites: PHYS 210A.

Elective SB-1: Biological Systems

Beng 211. systems biology and bioengineering i: biological components (4 units).

Components of biological systems, their biochemical properties and function. The technology used for obtaining component lists. Relationship within and integration of component lists. Structured vocabularies and component ontologies. Algorithms for comparative approaches in deciphering and mining component lists. Prerequisites: BENG 230A or BIMM 100, or consent of instructor. (F)

BENG 212. Systems Biology and Bioengineering II: Large-Scale Data Analysis (4 units)

Analysis of biological data can be performed at four levels: 1) statistical analysis, 2) integration of knowledge, 3) integration of networks, and 4) integration of biophysical laws. This course teaches the first two levels. The first level consists of specialized topics in statistical analysis of large-scale data sets and machine learning. The second level consists of leveraging prior knowledge for the analysis of diverse, multi-omic datasets and network reconstruction. Prerequisites: graduate standing. (W)

BENG 227. Transport Phenomena in Living Systems (4 units)

This course describes the movement of heat and chemical mass in biological systems. Diffusion, convection and biochemical reactions in a variety of biological and engineering examples are analyzed and modeled. Students that have taken BENG 222 cannot take BENG 227 for credit. Prerequisites: BENG 221, graduate standing, or consent of instructor. (S)

Elective SB-2: Kinetic Modeling

Beng 125. modeling and computation in bioengineering (4 units).

Computational modeling of molecular bioengineering phenomena: excitable cells, regulatory networks, and transport. Application of ordinary, stochastic, and partial differential equations. Introduction to data analysis techniques: power spectra, wavelets, and nonlinear time series analysis. Prerequisites: BENG 122A or BENG 123 or consent of department. (S)

BNFO 284. Nonlinear Dynamics in Quantitative Biology (4 units)

Qualitative, analytical and computational mathematical modeling techniques applied to regulatory networks and signaling networks. Stability, bifurcations, oscillations, multistability, hysteresis, multiple timescales, and chaos. Introduction to experimental data analysis and control techniques. Applications to synthetic biology, cellular population dynamics, ad canonical signaling networks (inflammation, tumor suppression, metabolism). Letter grades only. Prerequisites: bioinformatics and systems biology graduate students only.

PHYS 276. Quantitative Microbiology (4 units)

A quantitative description of bacteria from molecular interactions through cellular and population level behaviors. Topics will vary yearly, covering processes including gene regulation, molecular signaling, genetic circuits, stochastic dynamics, metabolic control, cell division, cell growth control, stress response, chemotaxis, biofilm formation. May be coscheduled with PHYS 176. Recommended preparation: an introductory course in biology is helpful but not necessary.

CHEM 220. Regulatory Circuits in Cells (4 units)

Modulation cellular activity and influencing viral fate involve regulatory circuits. Emergent properties include dose response, cross regulation, dynamic, and stochastic behaviors. This course reviews underlying mechanisms and involves mathematical modeling using personal computer tools. Recommended: some background in biochemistry and/or cellular biology. Mathematical competence at the level of lower-division college courses.

Elective BMI-1: Biomedical Informatics

Med 263. bioinformatics applications to human disease (4 units).

Students learn background knowledge and practical skills for investigating the biological basis for human disease. Using bioinformatics applications, they: (1) query biological and genetic sequence databases relevant to human health, (2) manipulate sequence data for alignment, recombination, selection, and phylogenetic analysis, (3) normalize microarray data and identify differentially expressed genes and biomarkers between patient groups, (4) annotate protein data and visualize protein structure, and (5) search the human genome and annotate genes relevant to human diseases. (W)

MED 264. Principles of Biomedical Informatics (4 units) – This core class for the BMI track may be taken as an elective for the BISB track.

Med 265. informatics in clinical environments (4 units).

Students are introduced to the basics of healthcare systems through direct observation and classroom discussion. Students are introduced to medical language, disease processes, and health care practices to provide context prior to direct patient observation at primary, specialty, emergency, and inpatient sites in conjunction with clinical faculty affiliated with the training program. Students examine how clinicians use history-taking, physical examination and diagnostic testing to establish diagnoses and prognoses. Medical decision-making is introduced in the context of available informatics tools and clinical documentation and communication processes. Post-observation classroom discussions encourage students to think critically of the processes they observed and formulate hypotheses about how informatics solutions can modify the processes. Students who already have a clinical background can substitute this course. (W)

MED 267. Modeling Clinical Data and Knowledge for Computation (4 units)

This course describes existing methods for representing and communicating biomedical knowledge. The course describes existing health care standards and modeling principles required for implementing data standards, including biomedical ontologies, standardized terminologies, and knowledge resources. (S, offered alternate years.)

MED 268. Statistics Concepts for Biomedical Research (4 units)

This course introduces statistics methods for basic, pre-clinical, and clinical research. Topics include descriptive statistics, t-tests, ANOVA, linear and logistic regression, survival analysis, power and sample size, non-parametric methods, and factorial experiment design. Emphasis is on applications rather than theorems and proofs. Students will gain the ability to design efficient and informative basic research and clinical trials, to perform statistical analyses using the R statistics software, and to critique statistical results in published biomedical research. (F) Prerequisites: Medical or Graduate Student

MED 276. Grant Proposal Writing Practicum (2 units)

The focus of this course will be on grant writing and developing persuasive arguments. Previously submitted funded and non-funded grants will be used to illustrate revision and response to reviewers, as well as to provide source materials to perform mock study section reviews. This course will help students write their first grant proposal and understand the process of proposal scoring and reviewing. (S, offered alternate years.)

MED 277. Introduction to Biomedical Natural Language Processing (4 units)

Biomedical Natural Language Processing (BioNLP) is an essential tool in both biomedical research and clinical applications. Students taking this course will learn how to process free text data and their integration with other types of biomedical data with BioNLP. (F)

Elective QBIO-1: Quantitative Biology

Beng 226. foundations of bioengineering i: tissue and cell properties (4 units).

Modern development of biomechanics at an advanced mathematical level. Description of internal stresses and deformation in living tissues and fluids, thermodynamics. Mechanics of soft connective tissue, extracellular matrix, cells, membranes, and cytoskeleton. Mechanotransduction, migration, adhesion. Blood flow in microvessels. Biomechanical analysis of tissue injury. Recommended preparation: a previous background in biomechanics is strongly recommended prior to taking this course. Prerequisites: graduate standing or consent of instructor. (S)

BENG 235. Molecular Imaging and Quantitation in Living Cells (4 units)

This course will introduce quantitative fluorescence microscopy techniques for imaging, manipulating, and quantifying the spatiotemporal characteristics of molecular events in live cells. A laboratory component will be integrated with students organized into small teams for projects. Recommended preparation: basic optics at the level of ECE 181, introductory molecular and cellular biology at the level of BIMM 100 and BICD 110, respectively. Prerequisites: graduate standing or consent of instructor. (S)

BGGN 214. Introduction to Q-Biology (4 units) – This may be applied to the BIO area elective requirement.

The course goal is to discuss and work through examples where quantitative biology approaches were necessary to yield novel biological insights. Problems will be presented with a historic perspective to instill a philosophy for when, how, and why q-bio approaches are most effective. The course may also appeal to physics and engineering graduate students. Prerequisites: graduate standing or consent of instructor.

BNFO 262/BIOM 262/BGGN 237/CMM 262. Quantitative Methods in Genetics (4 units)

This advanced problem-oriented course will examine experimental design, laboratory methods, and quantitative analytical tools used in genetic and genomic research. Students will analyze supplied data using a variety of software packages. Prerequisites: BGGN 223, or BIOM 252 and BIOM 272, or equivalent. Note: This was approved as an elective by the BISB Curriculum Committee, but it's still undergoing approval by other campus entities as part of a larger set of changes, including a new course number BNFO 262. BISB students should enroll in it as BNFO 262, once that's available. BNFO 262 / BIOM 262 / BGGN 237 will be cross-listed. Previously also numbered CMM 262.

MAE 263. Experimental Methods in Cell Mechanics (4 units)

Methods to measure mechanical aspects of cellular nature and behavior such as intracellular rheology, intracellular force distribution and propagation, cell adhesion strength, generation of propulsive forces during locomotion, interaction with the extracellular matrix, and response to external mechanical stimuli. Prerequisites: MAE 209 or MAE 210A, and graduate standing.

PHYS 273. Information Theory and Pattern Formation in Biological Systems (4 units)

This course discusses how living systems acquire information on their environment and exploit it to generate structures and perform functions. Biological sensing of concentrations, reaction-diffusion equations, the Turing mechanism, and applications of information theory to cellular transduction pathways and animal behavior will be presented. Recommended preparation: familiarity with probabilities at the level of undergraduate statistical mechanics and major cellular processes; basic knowledge of information theory.

PHYS 274. Stochastic Processes in Population Genetics (4 units)

The course explores genetic diversity within biological populations. Genetics fundamentals, mutation/selection equilibria, speciation, Wright-Fisher model, Kimura’s neutral theory, Luria-Delbrück test, the coalescent theory, evolutionary games and statistical methods for quantifying genetic observables such as SNPs, copy number variations, etc., will be discussed.  Recommended preparation: familiarity with probabilities and PDEs at the undergraduate level; an introduction to basic evolutionary processes.

PHYS 275. Biological Physics (4 units)

The course teaches how a few fundamental models from statistical physics provide quantitative explanatory frameworks for many seemingly unrelated problems in biology. Case studies rotate from year to year and may include ion channel gating, cooperative binding, protein-DNA interaction, gene regulation, molecular motor dynamics, cytoskeletal assembly, biological electricity, population and evolutionary dynamics. May be coscheduled with PHYS 175. Students in PHYS 275 are expected to complete a report at the level of a research paper.  Recommended preparation: an introduction to statistical mechanics, at least at the level of PHYS 140A or CHEM 132.

PHYS 277. Physics of the Cell (4 units)

Exploration of the physics problems that must be solved by a living cell in order to survive. Theoretical ideas from nonequilibrium statistical mechanics and dynamical systems are used to establish the physical principles that underlie biological function, focusing on the organization and behavior of eukaryotic cells. Specific topics rotate from year to year and may include genome organization and dynamics, motility, sensing, and organelle interaction. May be coscheduled with PHYS 177. The graduate version will include a report at the level of a research paper. Recommended preparation: familiarity with statistical mechanics at the level of PHYS 140A or CHEM 132.

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Chemistry MS Admissions

Thank you for your interest in the UC San Diego Chemistry & Biochemistry Graduate Program. We have over 300 bright and talented graduate students with diverse backgrounds from all over the world. We offer programs for the Doctoral, Masters, and Joint Doctoral degrees. Below you will find information on the needed application materials and criteria.

Application Deadlines

• MS Coursework and Thesis Admissions Deadline for Fall 2023 is January 10, 2024
• Deadline for Winter 2024 is October 25, 2023
• Deadline for Spring 2024 is January 10, 2024

General Application Information

To begin your online application or to check the status on your application, please visit  connect.grad.ucsd.edu/apply . Information you enter may be saved at any time.

The Admissions & Recruitment Committee recommends submitting your application as soon as you complete it, even if we have not yet received all your letters of recommendation. We also highly recommend that you answer some/all of our additional questions about your educational experiences.

We review PhD files continuously beginning in late November and try to get the good news out to those we are recruiting to our program as soon as possible. If you have yet to hear from us, your file is still pending a final decision.

Please note that submitting your application requires an associated application fee although under many circumstances you may request that this fee be waived. Please read the application fee link above and inquire with  [email protected]  if you have any questions or would like more information on the waiver options.

Transcripts

Statement of purpose.

We recommend that you structure your Statement of Purpose to address the following four prompts:

• Describe your personal and professional motivations for pursuing research in the field of chemistry and/or biochemistry.
• the overall context and importance of the work,
• the specific goal of the work you were doing, (c) the methods by which you worked to achieve those goals
• what you learned and what your new understanding means for the future of the project. Include a short discussion of how your research experience has shaped your decision to apply to our graduate program.
• Specify one or more faculty members in our department whose current research aligns with your interests. Provide some insight into why you made the choice(s) you did.
• Describe any obstacles that you have overcome to achieve your academic and personal achievements as well as any contributions to equity, diversity, and inclusion you have made.

If you are applying for the MS Coursework program, the research questions above might not apply.

We do not have a word limit, but we do recommend that you keep your statment of purpose clear and concise.

Letters of Recommendation

We  require three letters of recommendation. Letter writers that are able to provide context and clarity with respect to your ability and potential to excel in a graduate program are the most helpful in evaluating your application (e.g. a research advisor or a professors from a course that knows you well).

If your letter writer needs a new link to submit their letter, please follow the instructions below:

• Log into  online application
• Click “Update Application”
• Go to “Letters of Recommendation” page
• Click “Resend” next to the name of your letter writer

Additional Educational Experiences

Fee waiver programs.

There are a couple of fee waiver programs offered by the Division of Graduate Education and Postdoctoral Affairs (GEPA) and the Department of Chemistry and Biochemistry.

Please visit the GEPA website ( https://grad.ucsd.edu/admissions/requirements/application-fee-and-fee-waiver/index.html ) to see if you are eligible for a fee waiver with them. Follow their steps to request for one of their fee waivers. If you are not eligible for an application fee waiver through GEPA, then please follow the steps below to be considered for one of our limited number of fee waivers by our department.

• Please fill out the application as much as you can ( https://connect.grad.ucsd.edu/apply/ )
• Do not submit the application nor enter any payment information
• Take note of your application's reference number (you'll need that for the next step)
• Fill out our Fee Waiver Request Form to be considered ( https://forms.office.com/r/iWmHZXEE7B )
• The deadline to be considered for one of the department's application fee waivers is November 30, 2022.
• If selected for an application fee waiver, we will contact you with further instructions by December 5, 2022.

English Proficiency Exams (International Applicants Only)

Applicants that have recently studied full-time for one uninterrupted academic year at a university-level institution in which English is the language of instruction and in a country in which English is a dominant language, are exempt from language testing requirements.

Demonstrated proficiency in the English language (TOEFL, IELTS, or PTE) is required for all other international applicants whose native language is not English. Requirements for demonstrating proficiency are listed below.

International applicants must include an official report of their TOEFL iBT or TSE scores from  ETS . The university-wide minimum TOEFL score for graduate admission is  550 for the paper based test (PBT), and 85 for the internet based test (iBT) . The minimum for the   IELTS Academic Training exam is a score of 7   and a score of   65 for the PTE Academic.

At minimum, international applicants must also have a   TOEFL iBT Speaking subscore of 23 , an   IELTS Speaking subscore of 7 , or a   PTE Speaking subscores of 65 .

MS Thesis Agreement (MS Thesis Applicants Only)

Commitment to diversity.

The Department of Chemistry and Biochemistry welcomes all applicants. The university and department have a long-standing commitment to promoting equity, diversity and inclusion within STEM fields from. Our commitment to diversifying the scientific workforce also includes people who self-identify as members of the LGBTQ+ community, people of socio-economic disadvantaged backgrounds, and individuals with disabilities.

Outreach Conferences

National organization for the professional advancement of black chemists and engineers (nobcche).

September 26 - 29 | Orlando, FL

American Chemistry Society National Meeting

August 21-25 | Chicago, IL

American Indian Science and Engineering Society (AISES)

October 6-8, Palm Springs, CA

California Diversity Forum

November 5 | Long Beach, CA

Society for Advancement of Chicanos and Native Americans in Science (SACNAS)

October 27 - 29 | San Juan, PR

Annual Biomedical Research Conference for Minority Students (ABRCMS)

November 9 - 12 | Anaheim, CA

• ACS Bridge Program
• Degree Requirements
• Enrollment & Registration

Pioneering Science and Collaboration: Dr. Seema Mattoo's Trailblazing Journey

In the realm of academia, where disciplines often stand as distinct silos, Dr. Seema Mattoo, an Associate Professor of Biological Sciences at Purdue University, emerges as a trailblazer. Her journey, marked by resilience, curiosity, and a willingness to step outside her comfort zone, encapsulates the essence of groundbreaking scientific exploration.

A Journey Through Adversity and Academia  

Mattoo's journey began in Kashmir, India, a region steeped in diverse cultures and languages, but also marred by political conflict. Focused on education, her community's resilience in the face of adversity set the stage for her academic pursuits. During her second year of college, she and her family had to flee the genocide of her people in Kashmir, an experience that added a layer of depth to her commitment to education. The path led her to the University of Maryland and on to UCLA, where her graduate research led to the discovery of new aspects of bacterial virulence and aided in the development of the D-TaP vaccine for whooping cough.

From Vaccines to Cellular Mysteries: A Pivotal Shift  

While her early work addressed critical health issues, it was at UC San Diego and later at Purdue University that Mattoo pivoted from bacteria towards unraveling the intricate world of mammalian cellular mechanisms. Her multidisciplinary approach, blending microbiology, biochemistry, structural biology, and cell biology, set the stage for groundbreaking research - discovering a new class of enzymes called Fic proteins. Today, Fic proteins are recognized as key regulators of cellular communication in humans and other organisms.

Breakthroughs in Parkinson's Research

In the pursuit of understanding diseases linked to protein misfolding, Mattoo's team uncovered a potential breakthrough in aging related ailments like Parkinson's disease. The human Fic protein HYPE, a key regulator in cellular stress response, demonstrated the ability to modify alpha-synuclein (aSyn), reducing its aggregation. This discovery opens new avenues for preventive and therapeutic strategies, transcending traditional approaches to focus on the fundamental processes within cells. Her collaboration with Jean-Christophe Rochet, a professor of medicinal chemistry and molecular pharmacology, played an important role in advancing this Parkinson's research.

Transcending Disciplines: CryoAPEX Technique

Mattoo's commitment to interdisciplinary research manifested in the development of the cryoAPEX technique. Merging high-pressure freezing and chemical fixation, this innovative electron microscopy method allows for precise tracking of membrane proteins within well-preserved cells. Her work with cryoAPEX becomes a versatile tool for diverse researchers, fostering a new era in cellular imaging.

Navigating Challenges and Advocating for Inclusivity

As a woman of color in science, Mattoo navigates challenges with resilience and a commitment to inclusivity. Her experiences highlight the need for a supportive scientific community that doesn’t just recognize but also celebrates diversity within academia. Advocating for collaboration and leveraging diverse strengths, she embodies the transformative power of unity in advancing scientific understanding.

Her journey is not without its personal challenges. Small instances, like being the only woman in a meeting with assumptions about her role, and larger hardships that come with being a working mother, have tested her resilience. A colleague's comment during a challenging health crisis, suggesting that "this field is not meant for a woman," reflects the broader hurdles women in science still face. While acknowledging the difficulties, Mattoo also emphasizes the progress made and the importance of supporting the next generation. She believes in the generosity of a fellowship of scientists, striving to pave the way and eliminate hurdles for those who follow.

Mentoring and Teaching Innovation

Mattoo credits much of success to some of the most hardworking, dedicated students who joined her early lab, notably Anwesha Sanyal, Hee-Jeong Kim and Ben Watson. In addition to graduate students and Postdocs, Matto’s lab is very popular with undergraduates interested in research. She has trained nearly 50 undergrads, several of whom have graduated with an Honors Thesis and with authorship on publications. All of her trainees (undergrad to postdocs) routinely win awards, including the prestigious Barry Goldwater Fellowship. These aspects of training and love for scientific enquiry extend beyond the lab and into the classroom. Her Medical Microbiology course has functioned as a CURE (Curriculum-based Undergraduate Research Experience), and she has incorporated AI and the use of ChatGPT into the curriculum. Mattoo’s was one of the first courses in the Life Sciences to adopt AI. She also teach ethics and responsible conduct of research, and is part of the Elevate program which fosters inclusion through team activities in the classroom.

Unlocking a Blueprint for Health: The ER as a Disease Safeguard  

Mattoo's commitment to advancing her research extends beyond traditional academic avenues. In response to a funding competition through the Life Sciences Summit, an exciting initiative by Purdue to develop synergies across various research areas  to tackle a critical health related challenge, she successfully led a team to secure a winning spot.

Mattoo’s presentation at the Life Sciences Summit was entitled "Unlocking a Blueprint for Health: The Endoplasmic Reticulum (ER) as a Disease Safeguard." Collaborating with a diverse team including Vikki Weake, Bryon Drown, Fang Huang, Christina Ferriera, Jonathan Schlebach, Rams Subramanian, Eugenio Culurciello, Daniel Flaherty, and Alex Chortos, her proposal focuses on understanding the fundamental steps crucial for protein folding within the ER.

A Testament to Curiosity and Collaboration

Dr. Seema Mattoo's journey within the College of Science at Purdue University stands as a testament to the transformative power of curiosity, collaboration, and resilience. Her amassed expertise from bacteriology to unraveling scientific mysteries in human cells, combined with a commitment to teaching, mentoring, and inclusivity, positions her as a beacon of inspiration for the scientific community. Such an unconventional path is rarely easy or quick. Mattoo is grateful to the many supporters in her journey who held faith in her abilities. One such recognition came in late 2022 when she was selected as one of six scientists for the inaugural class of the Hypothesis Fund, an innovative funding mechanism that identifies and promotes “bold new ideas in basic research”. As she continues to unlock the secrets within cells, Mattoo's work reflects the spirit of innovation that defines Purdue University's legacy in pushing the boundaries of scientific exploration.

About the Department of Biological Sciences at Purdue University

Purdue University's Department of Biological Sciences is committed to conducting innovative research that addresses pressing challenges in the life sciences. What we do is biology at scales. With a focus on interdisciplinary collaboration and cutting-edge technologies, our faculty and students are at the forefront of discovery and innovation. We provide life changing education and game changing research. Learn more at   bio.purdue.edu/ .

Writer: Alisha Referda, [email protected]

Purdue University Biological Sciences, 915 Mitch Daniels Boulevard, West Lafayette, IN 47907

Main Office: (765) 494-4408   Business Office: (765) 494-4764   Contact Us

© 2024 Purdue University | An equal access/equal opportunity university | Copyright Complaints

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Research Associate - 128707

Job description, #128707 research associate.

This position will remain open until a successful candidate has been identified.

UCSD Layoff from Career Appointment : Apply by 03/15/2024 for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor.

Special Selection Applicants : Apply by 03/26/2024. Eligible Special Selection clients should contact their Disability Counselor for assistance.

DESCRIPTION

The Moores Cancer Center (MCC) is one of just 55 NCI-designated Comprehensive Cancer Centers in the United States and the only one in San Diego County. As a consortium cancer center, it is a collaborative partnership between the UCSD: encompassing 28 departments, 6 schools (School of Medicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, School of Public Health, Jacobs School of Engineering, School of Biological Sciences & the School of Physical Sciences), UCSD Health oncology hospitals and clinics; the basic and public health research and outreach of San Diego State University (SDSU), and the basic and translational research of the La Jolla Institute of Immunology (LJI). These various programs and units are all dedicated to fulfilling the Moores Cancer Center's mission of reducing cancer's burden. As such, it ranks among the top centers in the nation conducting the continuum of cancer research, providing advanced patient care, and serving the community through outreach and education programs. As a top-ranking, future-oriented organization, we offer challenging career opportunities in a fast-paced and innovative environment. Moores Cancer Center follows a progressive philosophy of career-path development for its employees including opportunities for cross-training, professional development, and progressive responsibility.

MCC's mission is to transform cancer care in our catchment area and beyond by driving exceptional scientific discoveries and innovations in prevention, detection, care, and training. MCC will make a global impact on improving health by reducing cancer burden through accelerated discovery and translation, compassionate and interdisciplinary care, education and community engagement, with the foundation of our core values - Excellence, Innovation and Risk-Taking, Collaboration, Diversity and Service.

Perform tumor immunology studies consisting of murine models of cancer, animal breeding and genotyping, flow cytometry, single cell sequencing, immunohistochemistry, in vitro cell biology, and in vitro biochemistry. Murine tumor biology studies will include xenograft, orthotopic and spontaneous tumor growth and metastasis assays, immunological analysis, treatment of animals with experimental therapeutic agents by gavage, intravenous and intraperitoneal methods, breeding and genotyping of transgenic and mutant mice, and immune cell isolations. Perform major surgery, including small animal anesthesia. In addition, perform immunohistochemistry of frozen and fixed tissues or cells. Conduct various in vitro cell biology techniques to include performing flow cytometry analysis of cell surface protein expression, cell adhesion and migration assays, transfecting cells with expression constructs, preparing lysates of cells in culture or tissues, quantification, ELISA assays, SDS PAGE, Western and Immunoblotting and gel electrophoresis. Additionally, perform recombinant DNA techniques to include preparing plasmids and maintaining plasmid stocks, analyzing DNA and RNA purification, and conducting DNA electrophoresis, and RT-PCR. Make innovative contributions regarding experimental design and methodology, using published scientific data in referred journals, as well as online using search engines and subject-specific websites, to make recommended changes to current protocols and practices. Troubleshoot problems for quality control on immunochemical and histochemical procedures. Maintain and prepare accurate records of all experiments. Assist in the preparation of data for publication. Assume responsibility for lab maintenance and safety training. Provide training and work direction in areas of expertise as needed. Maintain and prepare accurate records of all experiments. Assist in the preparation of data for publication. Other duties assigned as needed.

MINIMUM QUALIFICATIONS

Advanced theoretical knowledge of molecular biology, biochemistry, physiology and cell biology or a Bachelor’s of Science degree in an appropriated field of science or equivalent in education and experience.

Experience independently isolating bone marrow and blood cells for analysis by flow cytometry, immunoblotting, gene expression and cell adhesion assays.

Experience independently performing and directing in vivo experiments including the injection of growth factors, tumor cells and therapeutics, bleeding and tissue harvesting of mice and in performing minor surgery.

Experience independently performing and directing protein analysis techniques including protein determination, ELISA and Magpix assays and protein separation techniques.

Experience independently working with endothelial, myeloid and tumor cell culture, DNA and RNA isolation from culture cells and from tissues, immunoblotting and quantitative RT-PCR for genes and proteins that regulate myeloid cell adhesion, migration and gene and protein expression in vitro and in vivo.

Experience independently developing improvements to tissue culture techniques, including sterile technique, cell adhesion and migration assays.

Experience performing independently performing and directing molecular biological techniques, including DNA purification, genotyping and cloning.

Enthusiasm for learning and a genuine interest in scientific research. Willingness and ability to learn new skills, research methods, and scientific principles. Experience and interest in developing novel techniques and analytical methods.

Ability to develop new experimental procedures with accuracy and efficiency and to teach others to perform them with accuracy.

Ability to use basic and advanced laboratory equipment, including centrifuges, spectrophotometers, balances pH meters, electrophoresis, single cell sequencing, magnetic and light based plate readers and flow cytometers equipment.

Ability to write and follow step wise experimental protocols.

Willingness and ability to handle mice for surgical procedures, including anesthesia administration. Experience to maintain animal colony by breeding, genotyping and weaning animals, creating new animal strains and keeping accurate records

Strong communication skills (both verbal and written) needed to interact professionally and effectively in the work environment, as well as to effectively and accurately document research procedures. Ability to read, comprehend, and discuss research materials.

Ability to adhere to established UCSD guidelines for safety and environmental issues.

Experience with personal computers, including word processing and spreadsheets. Ability to use Quartzy and Oracle to place and reconcile orders and receipts.

Ability to maintain confidentiality.

Experience managing laboratory, including directing student employees and volunteers, ordering and maintaining inventory., organizing and maintaining freezers, cold room, and equipment.

Knowledge to manage official travel and entertainment documentation and file reimbursements requests.

Demonstrated knowledge in making innovative contributions to experimental design and methodology.

Interest and ability to teach students, postdocs and new personnel methods and skills.

Demonstrated ability use and adapt existing techniques and technologies in novel and non-traditional ways in order to meet research objectives.

SPECIAL CONDITIONS

Employment is subject to a criminal background check.

Must be willing to work frequently with animals and to work occasional nights and weekends.

Proven ability to work with animals and willingness to work with biohazardous materials.

Pay Transparency Act

Annual Full Pay Range: $64,506 - $103,727 (will be prorated if the appointment percentage is less than 100%)

Hourly Equivalent: $30.89 - $49.68

Factors in determining the appropriate compensation for a role include experience, skills, knowledge, abilities, education, licensure and certifications, and other business and organizational needs. The Hiring Pay Scale referenced in the job posting is the budgeted salary or hourly range that the University reasonably expects to pay for this position. The Annual Full Pay Range may be broader than what the University anticipates to pay for this position, based on internal equity, budget, and collective bargaining agreements (when applicable).

If employed by the University of California, you will be required to comply with our Policy on Vaccination Programs, which may be amended or revised from time to time. Federal, state, or local public health directives may impose additional requirements. If applicable, life-support certifications (BLS, NRP, ACLS, etc.) must include hands-on practice and in-person skills assessment; online-only certification is not acceptable.

UC San Diego Health Sciences is comprised of our School of Medicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, The Herbert Wertheim School of Public Health and Human Longevity Science, and our Student Health and Well-Being Department. We have long been at the forefront of translational - or "bench-to-bedside" - research, transforming patient care through discovery and innovation leading to new drugs and technologies. Translational research is carried out every day in the hundreds of clinical trials of promising new therapies offered through UC San Diego Health, and in the drive of our researchers and clinician-scientists who are committed to having a significant impact on patient care. We invite you to join our team!

Applications/Resumes are accepted for current job openings only. For full consideration on any job, applications must be received prior to the initial closing date. If a job has an extended deadline, applications/resumes will be considered during the extension period; however, a job may be filled before the extended date is reached.

To foster the best possible working and learning environment, UC San Diego strives to cultivate a rich and diverse environment, inclusive and supportive of all students, faculty, staff and visitors. For more information, please visit UC San Diego Principles of Community .

UC San Diego Health is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability, age, protected veteran status, gender identity or sexual orientation. For the complete University of California nondiscrimination and affirmative action policy see: http://www-hr.ucsd.edu/saa/nondiscr.html

UC San Diego is a smoke and tobacco free environment. Please visit smokefree.ucsd.edu for more information.

UC San Diego Health maintains a marijuana and drug free environment. Employees may be subject to drug screening.

Application Instructions

Please click on the link below to apply for this position. A new window will open and direct you to apply at our corporate careers page. We look forward to hearing from you!

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Posted : 4/8/2024

Job Reference # : 128707

JOIN OUR TALENT COMMUNITY

Interested in working at UC San Diego and UC San Diego Health but can't find a position that's right for you? Submit your resume to our Talent Community to be considered for future opportunities that may align with your expertise. Please note, by joining our Talent Community, you are not applying for a position with UC San Diego Campus and Health. Rather, this is an additional way for our Talent Acquisition team to find candidates with specific credentials, if an opportunity arises. You are still encouraged to regularly check back on our career site or sign up for Job Alerts to apply for openings that are a match for your background.

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Welcome to Sixth College! The lead team consists of five individuals who are working together to collaborate and plan the logistic side of orientation. 

Katie Perullo

Pronouns: she/her/hers

Email:  [email protected]

Position:  Senior New Student Program Specialist

Fun Fact:  I recently completed the LA Marathon in March!

Angelien Nguyen

Email:  [email protected]

Position:  Orientation Undergraduate Intern

Major:  International Business

Year: 3rd Year

Involvements: Sixth College Student Council (Festival Director), Vietnamese Eucharistic Youth Movement, Campus Events (Event & Marketing Assistant)

Fun Fact:  I met Oprah, Selena Gomez, Alicia Keys, and Ali Wong all on the same day.

Angelien is also a first generation student and commuter. 

Kriscia Uson

Email:   [email protected]

Position:  Senior Orientation Leader

Major:  Public health with a concentration in medicine

Involvements:  Ascension Competitive Dance Team, Division 12 Dance Team, Dance Co-Coordinator Kaibigang Pilipin@

Fun Fact:  I've been stuck in a desert.

Alexander Edwards

Pronouns: h e/him/his

Email:  [email protected]

Position: Senior  Orientation Leader

Major:  Marine Biology

Minor: Environmental Studies

Year: 4th Year

Fun Fact:  I enjoy cooking and trying new recipes. 

Alexander is also a transfer student and commuter. 

Annie Nguyen

Email:  [email protected]

Major:  Political Science (Public Law)

Minor: Business Economics

Year: 2nd Year

Involvements:  Chancellor's Scholar Alliance and Retirement Resource Center

Fun Fact:  My favorite song is All Too Well (10 Minute Version) by Taylor Swift!

Annie is also a first generation student.

Orientation Leader

Our Orientation Leaders are students who will be guiding you throughout the Part III: In-Person Orientation. Your OLs are excited to get to know you and are open to sharing their advise and experience on their transition to college.  

Meet the team soon!

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• First Year Student Orientation
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