CEMI’s version of microbiology education is unique. Faculty from multiple divisions work together to train students in how to understand microbial systems at various spatial and temporal scales: from the molecular to the global, from the present to the past. This interdisciplinary training involves the study of molecular and cellular biology, physiology, chemistry, ecology, and quantitative reasoning. Students can enter the CEMI program from a variety of graduate programs, including, but not limited to: Biology, Bioengineering, Chemistry, Chemical Biology, Biochemistry and Molecular Biophysics, Geobiology and Geochemistry. The course requirements for each option vary, but CEMI core courses are open to all. CEMI faculty from any department at Caltech can nominate an incoming graduate student to receive a CEMI 1st year fellowship. Click here for a list of previous awardees.
In addition to offering core courses in microbiology, the CEMI occasionally sponsors workshops to fill particular needs. Any member of the CEMI community is welcome to suggest a topic for a workshop. Please contact the CEMI administrator if you have an idea. Click here for a list of workshops we have sponsored.
UndergraduatesTo apply to Caltech, visit the Undergraduate Admissions website. If you are already at Caltech and interested in microbiology, check out the CEMI faculty list and contact the PIs whose research most interests you. You could get involved in research during the academic year, or in the summer through the following programs:
Undergraduate Summer Research Opportunities
Graduate Options for Microbiology
Students interested in microbiology can pursue their interests through one of several graduate options:
- Biochemistry and Molecular Biophysics
- Chemical Engineering
- Environmental Science and Engineering
- Geological and Planetary Sciences
Applicants must have completed a bachelor's degree or the equivalent before beginning graduate study. Applicants who already possess a Ph.D. degree will generally not be considered for a second Ph.D. degree. Transcripts, GRE scores, letters of recommendation, and the applicant's statement of purpose are all required components of the application and are carefully weighed during the evaluation process. The admissions committee may also consider research papers, publications and other original work.
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- DOE Science Graduate Fellowship
- EPA Fellowship Program
- Ford Foundation Predoctoral Fellowship
- HHMI Science Education Grants Program
- NDSEG National Defense Science and Engineering Graduate Fellowship
- NSF Graduate Research Fellowship Program
- Switzer Environmental Fellowship
Postdoctoral scholars are valued members of the CEMI community. If you are considering coming to Caltech as a postdoc, please contact the PI of the CEMI group you are interested in, and consider applying for one of the following fellowships to help support your work while you are here. Click this link for more information about postdoctoral life at Caltech.
- ACS Postdoctoral Fellowships
- Agouron Institute Postdoctoral Fellowships
- AHA Postdoctoral Fellowships
- Cystic Fibrosis Foundation Postdoctoral Research Fellowships
- Damon Runyon Cancer Research Foundation Fellowship
- Ford Foundation Postdoctoral Fellowships
- Environmental Science and Engineering (ESE)
- Helen Hay Whitney Foundation Postdoctoral Fellowships
- Human Frontier Science Program Postdoctoral Fellowships
- Jane Coffin Childs Memorial Fund for Medical Research Fellowship
- Life Sciences Research Foundation Postdoctoral Fellowship
- L’Oréal USA Fellowships for Women in Science Program
- NASA Postdoctoral Program Opportunities
- NIH Individual Postdoctoral Fellowships (F32)
- NSF Minority Postdoctoral Research Fellowships
- O.K. Earl Postdoctoral Fellowship and the Texaco Postdoctoral Fellowship
- USGS Mendenhall Research Fellowship
Microbiology Core Courses
Bi 116. Microbial Genetics. 9 units (3-0-6); second term. Prerequisites: Bi 1, 8, 9 (or equivalent), and ESE/Bi 166. A course on microbial genetics, emphasizing the history of the discipline as well as modern approaches. Students will be exposed to different ways of manipulating microbial genomes (primarily bacterial, but we will also cover archaea and microbial eukaryotes). The power of microbial genetics to shed light on diverse process will be discussed in a variety of contexts, ranging from environmental science to the mammalian microbiome. Instructors: Mazmanian, Newman. Given in alternate years; offered 2019–20.
Bi 165. Microbiology Research: Practice and Proposal. 6 units (2-3-1); first term. TThe course will serve to introduce graduate students to 1) the process of writing fellowships to train students in preparing effective funding applications; 2) ongoing research projects on campus involving the isolation, culture, and characterization of microbes and microbial communities as well as projects in other fields; and 3) presentation of research and asking questions in research presentations. The first half of the class will involve training in grant writing by drafting an NSF-GRFP proposal. The second half of the class will involve giving chalk talk research presentations. Students can apply from all departments; priority will be given to those in microbiology. Enrollment is limited to instructor approval. Instructor: Hoy.
ESE/Bi 166. Microbial Physiology. 9 units (3-1-5); first term. A course on growth and functions in the prokaryotic cell. Topics covered: growth, transport of small molecules, protein excretion, membrane bioenergetics, energy metabolism, motility, chemotaxis, global regulators, and metabolic integration. Instructor: Leadbetter.
ESE/Bi 168. Microbial Metabolic Diversity. 9 units (3-0-6); second term. Prerequisites: ESE 142, ESE/Bi 166. A course on the metabolic diversity of microorganisms. Basic thermodynamic principles governing energy conservation will be discussed, with emphasis placed on photosynthesis and respiration. Students will be exposed to genetic, genomic, and biochemical techniques that can be used to elucidate the mechanisms of cellular electron transfer underlying these metabolisms. Instructor: Newman.
Ge/ESE 170. Microbial Ecology. 9 units (3-2-4); third term. Prerequisite: ESE/Bi 166. Structural, phylogenetic, and metabolic diversity of microorganisms in nature. The course explores microbial interactions, relationships between diversity and physiology in modern and ancient environments, and influence of microbial community structure on biogeochemical cycles. Introduction to ecological principles and molecular approaches used in microbial ecology and geobiological investigations. Instructor: Orphan.
Bi/BE/Ch/ChE/Ge 269. Integrative Projects in Microbial Science and Engineering. 6 units (3-0-3); second term. A project-based course designed to train students to integrate biological, chemical, physical and engineering tools into innovative microbiology research. Students and faculty will brainstorm to identify several “grand challenges” in microbiology. Small teams, comprised of students from different graduate programs and disciplinary backgrounds (e.g. a chemical engineer, a computer scientist and a biologist) and a faculty member, will work to compose a project proposal addressing one of the grand challenges, integrating tools and concepts from across disciplines. Student groups will present draft proposals and receive questions and critiques from other members of the class at check-in points during the academic term. While there will not be an experimental laboratory component, project teams may tour facilities or take field trips to help define the aims and approaches of their projects. At the end of the course, teams will deliver written proposals and presentations that will be critiqued by students and faculty. Instructor: CEMI Faculty.
Biochemistry and Molecular Biophysics (BMB)
BMB/Bi/Ch 170 abc. Biochemistry and Biophysics of Macromolecules and Molecular Assemblies. 9 units (3-1-5); first, second, third terms. Prerequisite: Bi/Ch 110. First term: detailed analysis of the structures of the four classes of biological molecules and the forces that shape them. Introduction to molecular biological and visualization techniques. Second term: basic principles of modern biophysical and structural methods to interrogate macromolecules from the atomic to cellular levels, including X-ray crystallography, NMR spectroscopy, molecular dynamics, electron and light microscopy, AFM, single molecule techniques, and systems biological simulations. Third term: detailed analysis of specific macromolecular machines and systems that illustrate the principles and biophysical methods taught in the first two terms. Instructors: Clemons, Jensen, Shan, Hoelz, staff.
BE/APh 161. Physical Biology of the Cell. 12 units (3-0-9); second term. Prerequisites: Ph 2ab and ACM 95abc, or background in differential equations and statistical and quantum mechanics, or instructor’s written permission. Physical models applied to the analysis of biological structures ranging from individual proteins and DNA to entire cells. Topics include the force response of proteins and DNA, models of molecular motors, DNA packing in viruses and eukaryotes, mechanics of membranes, and membrane proteins and cell motility. Instructor: Phillips.
BE 262. Physical and Synthetic Biology Boot Camp. 9 units (1-8-0); third term. This course provides an intensive research introduction to current projects in physical and synthetic biology. Projects are based on current research directions in participating labs, including those of visiting biologists invited for the course. Representative classes of experiments include quantitative fluorescent microscopy of cell and organelle dynamics, single-cell measurement of genetic expression levels during development, and design and construction of biological circuits in microbes. Graded pass/fail. Instructor: Phillips.
Bi 1 x. The Great Ideas of Biology: An Introduction through Experimentation. 9 units (0-6-3); third term. Introduction to concepts and laboratory methods in biology. Molecular biology techniques and advanced microscopy will be combined to explore the great ideas of biology. This course is intended for nonbiology majors and will satisfy the freshman biology course requirement. Limited enrollment. Instructor: Bois.
Bi 114. Immunology. 9 units (3-0-6); second term. Prerequisites: Bi 8, Bi 9, Bi 122 or equivalent, and Bi/Ch 110 recommended. The course will cover the molecular and cellular mechanisms that mediate recognition and response in the mammalian immune system. Topics include cellular and humoral immunity, the structural basis of immune recognition, antigen presentation and processing, gene rearrangement of lymphocyte receptors, cytokines and the regulation of cellular responses, T and B cell development, and mechanisms of tolerance. The course will present an integrated view of how the immune system interacts with viral and bacterial pathogens and commensal bacteria. Instructors: Bjorkman, Yui.
Bi 190. Systems Genetics. 6 units (2-0-4); third term. Prerequisites: Bi 122. Lectures covering how genetic and genomic analyses are used to understand biological systems. Emphasis is on genetic and genome-scale approaches used in model organisms such as yeast, flies, worms, and mice to elucidate the function of genes, genetic pathways and genetic networks. Given in alternate years; not offered 2019-20. Instructor: Sternberg.
Bi/CNS/NB 250 c. Topics in Systems Neuroscience. 9 units (3-0-6); third term. Prerequisite: graduate standing. The class focuses on quantitative studies of problems in systems neuroscience. Students will study classical work such as Hodgkin and Huxley's landmark papers on the ionic basis of the action potential, and will move from the study of interacting currents within neurons to the study of systems of interacting neurons. Topics will include lateral inhibition, mechanisms of motion tuning, local learning rules and their consequences for network structure and dynamics, oscillatory dynamics and synchronization across brain circuits, and formation and computational properties of topographic neural maps. The course will combine lectures and discussions, in which students and faculty will examine papers on systems neuroscience, usually combining experimental and theoretical/modeling components. Instructor: Siapas.
Bi/BMB 251 abc. Current Research in Cellular and Molecular Biology. 1 unit. Prerequisite: graduate standing. Presentations and discussion of research at Caltech in biology and chemistry. Discussions of responsible conduct of research are included. Instructors: Sternberg, Hay.
Chemical Engineering (ChE)
ChE 101. Chemical Reaction Engineering. 9 units (3-0-6); second term. Prerequisites: ChE 62 and ChE 63 ab, or instructor’s permission. Elements of chemical kinetics and chemically reacting systems. Homogeneous and heterogeneous catalysis. Chemical reactor analysis. Instructor: Arnold.
ChE/BE 163. Introduction to Biomolecular Engineering. 9 units (3-0-6); first term. Prerequisites: Bi/Ch 110 or instructor’s permission.The course introduces rational design and evolutionary methods for engineering functional protein and nucleic acid systems. Rational design topics include molecular modeling, positive and negative design paradigms, simulation and optimization of equilibrium and kinetic properties, design of catalysts, sensors, motors, and circuits. Evolutionary design topics include evolutionary mechanisms and tradeoffs, fitness landscapes, directed evolution of proteins, and metabolic pathways. Some assignments require programming (MATLAB or Python). Instructors: Arnold, Pierce.
Geological and Planetary Sciences (Ge)
Ge/ESE 143. Organic Geochemistry. 9 units (3-2-4); first term. Prerequisite: Ch 41 a or equivalent. Main topics include the analysis, properties, sources, and cycling of natural organic materials in the environment, from their production in living organisms to burial and decomposition in sediments and preservation in the rock record. Specific topics include analytical methods for organic geochemistry, lipid structure and biochemistry, composition of organic matter, factors controlling organic preservation, organic climate and CO2 proxies, diagenesis and catagenesis, and biomarkers for ancient life. A laboratory component (three evening labs) teaches the extraction and analysis of modern and ancient organic biomarkers by GC/MS. Class includes a mandatory one-day (weekend) field trip to observe the Monterey Formation. Instructor: Sessions. Given in alternate years.
Ge 145. Isotope-Ratio Mass Spectrometry. 9 units (1-4-4); first term. This class provides a hands-on introduction to the construction and operating principles of instrumentation used for isotope-ratio mass spectrometry. The class is structured as a 1-hour lecture plus 4-hour lab each week examining the major subsystems of an IRMS, including vacuum systems, ionization source, mass analyzer, and detector. Laboratories involve hands-on deconstruction and re-assembly of a retired IRMS instrument to examine its components. Course is limited to 6 students at the discretion of the instructor, with preference given to graduate students using this instrumentation in their research. Instructor: Sessions.
Ge/Bi 246. Molecular Geobiology Seminar. 6 units (2-0-4); second term. Recommended preparation: ESE/Bi 166. Critical reviews and discussion of classic papers and current research in microbiology and geomicrobiology. As the topics will vary from year to year, it may be taken multiple times. Instructor: Orphan. Given in alternate years.