Biology
BIO 200: Advanced Molecular Biology (BIO 104)
Molecular mechanisms that govern the replication, recombination, and expression of eukaryotic genomes. Topics: DNA replication, DNA recombination, gene transcription, RNA splicing, regulation of gene expression, protein synthesis, and protein folding. Prerequisite: Biology core.
Terms: Win | Units: 5
Instructors: Frydman, J.; Gozani, O.
BIO 203: Advanced Genetics (DBIO 203, GENE 203)
For graduate students in Bioscience programs; may be appropriate for graduate students in other programs. The genetic toolbox. Examples of analytic methods, genetic manipulation, genome analysis, and human genetics. Emphasis is on use of genetic tools in dissecting complex biological pathways, developmental processes, and regulatory systems. Faculty-led discussion sections with evaluation of papers. Students with minimal experience in genetics should prepare by working out problems in college level textbooks.
Terms: Aut | Units: 4
Instructors: Kim, S.; Sidow, A.; Stearns, T.
BIO 205: DNA Repair and Genomic Stability
Interactions of endogenous and environmental mutagens with cellular DNA. Cellular responses to damaged DNA including molecular mechanisms for DNA repair, translesion DNA synthesis, and genetic recombination. Inducible repair responses and error-prone mechanisms. Human hereditary diseases that predispose to cancer. Relationships of DNA repair to mutagenesis, carcinogenesis, aging, and human genetic disease. Current research literature. Prerequisites: 41 and 118, or consent of instructor.
Terms: Spr | Units: 3
Instructors: Ford, J.; Hanawalt, P.
BIO 206: Field Studies in Earth Systems (EARTHSYS 189)
For advanced upper-division undergraduates and graduate students. Field-based, focusing on the components and processes by which terrestrial ecosystems function. Topics from biology, chemistry, ecology, geology, and soil science. Lecture, field, and lab studies emphasize standard field techniques, experimental design, analysis of data, and written and oral presentation. Small team projects test the original questions in the functioning of natural ecosystems. Admission by application; see Axess. Prerequisites: BIO 141 or EESS 160 (formerly GES 160), or equivalent.
Terms: alternate years, given next year | Units: 5
BIO 207: Life and Death of Proteins
How proteins are made and degraded in the cell. Discussion of primary literature. Case studies follow the evolution of scientific ideas, and evaluate how different experimental approaches contribute to our understanding of a biological problem. Emphasis on multidisciplinary approaches. Topics: protein folding and assembly, mechanisms of chaperone action, sorting into organelles, misfolding and disease, and the ubiquitin-proteasome pathway. Enrollment limited to 30.
Terms: Win | Units: 3
Instructors: Frydman, J.
BIO 209A: The Human Genome and Disease (BIO 109A, HUMBIO 158)
The variability of the human genome and the role of genomic information in research, drug discovery, and human health. Concepts and interpretations of genomic markers in medical research and real life applications. Human genomes in diverse populations. Original contributions from thought leaders in academia and industry and interaction between students and guest lecturers.
Terms: Win | Units: 3
Instructors: Heller, R.
BIO 209B: The Human Genome and Disease: Genetic Diversity and Personalized Medicine (BIO 109B)
Continuation of 109A/209A. Genetic drift: the path of human predecessors out of Africa to Europe and then either through Asia to Australia or through northern Russia to Alaska down to the W. Coast of the Americas. Support for this idea through the histocompatibility genes and genetic sequences that predispose people to diseases. Guest lectures from academia and pharmaceutical companies. Prerequisite: Biology or Human Biology core.
Terms: Spr | Units: 3
Instructors: Heller, R.
BIO 212: Human Physiology (BIO 112, HUMBIO 133)
The functioning of organ systems emphasizing mechanisms of control and regulation. Topics: structure and function of endocrine and central nervous systems, cardiovascular physiology, respiration, salt and water balance, exercise, and gastrointestinal physiology. Prerequisite: Biology or Human Biology core.
Terms: Win | Units: 4
Instructors: Garza, D.
BIO 213: Biology of Viruses
Principles of virus growth, genetics, architecture, and assembly. The relation of temperate viruses and other episomes to the host cell. Prerequisite: Biology core. Recommended: 118.
Terms: Win | Units: 3
Instructors: Campbell, A.
BIO 214: Advanced Cell Biology (BIOC 224)
For Ph.D. students. Current research on cell structure, function, and dynamics. Topics include complex cell phenomena such as cell division, apoptosis, compartmentalization, transport and trafficking, motility and adhesion, differentiation, and multicellularity. Current papers from the primary literature. Prerequisite for advanced undergraduates: BIO 129A,B, and consent of instructor.
Terms: Win | Units: 2-5
Instructors: Kopito, R.; Nachury, M.; Pfeffer, S.; Straight, A.; Theriot, J.
BIO 215: Biochemical Evolution
Biochemical viewpoints on the evolutionary process. Topics: prebiotic biochemistry and the origins of life; adaptive organization of metabolism; enzyme polymorphisms and other biochemical aspects of population genetics; macromolecular phylogeny and protein clocks. Prerequisites: Biology core or substantial equivalent.
Terms: alternate years, given next year | Units: 3
BIO 216: Terrestrial Biogeochemistry
Nutrient cycling and the regulation of primary and secondary production in terrestrial, freshwater, and marine ecosystems; land-water and biosphere-atmosphere interactions; global element cycles and their regulation; human effects on biogeochemical cycles. Prerequisite: graduate standing in science or engineering; consent of instructor for undergraduates or coterminal students.
Terms: alternate years, given next year | Units: 3
BIO 217: Neuronal Biophysics
Biophysical descriptions and mechanisms of passive and excitable membranes, ion channels and pumps, action potential propagation, and synaptic transmission. Introduction to dynamics of single neurons and neuronal networks. Emphasis is on the experimental basis for modern research applications. Interdisciplinary aspects of biology and physics. Literature, problem sets, and student presentations. Prerequisites: undergraduate physics, calculus, and biology.
Terms: Win | Units: 4
Instructors: Schnitzer, M.
BIO 218: Genetic Analysis of Biological Processes (BIO 118)
Genetic principles and their experimental applications. Emphasis is on the identification and use of mutations to study cellular function. Prerequisite: Biology core.
Terms: Spr | Units: 5
Instructors: Green, E.; Reinhart, B.
BIO 222: Exploring Neural Circuits
Seminar. The logic of how neural circuits control behavior; how neural circuits are assembled during development and modified by experience. Emphasis is on primary literature. Topics include: neurons as information processing units; simple and complex circuits underlying sensory information processing and motor control; and development and plasticity of neural circuits. Advanced undergraduates with background in physical science, engineering, and biology may apply to enroll. Recommended: background in neuroscience.
Terms: not given this year | Units: 3
BIO 223: Stochastic and Nonlinear Dynamics (APPPHYS 223)
Theoretical analysis of dynamical processes: dynamical systems, stochastic processes, and spatiotemporal dynamics. Motivations and applications from biology and physics. Emphasis is on methods including qualitative approaches, asymptotics, and multiple scale analysis. Prerequisites: ordinary and partial differential equations, complex analysis, and probability or statistical physics.
Terms: Spr, alternate years, not given next year | Units: 3
Instructors: Fisher, D.
BIO 230: Molecular and Cellular Immunology
For advanced undergraduate and graduate students. Components of the immune system and mechanisms of immune responses: structure, function, and genetics of antibody molecules; cellular basis of immunity and its regulation; molecular biology and biochemistry of antigen receptors and signaling pathways; genetic control of immunity and disease susceptibility. Emphasis is on key experimental approaches. Prerequisite for undergraduates: Biology or Human Biology core, or consent of instructor.
Terms: Aut | Units: 4
Instructors: Jones, P.
BIO 230A: Molecular and Cellular Immunology Literature Review
Special discussion section for graduate students. Supplement to 230. Corequisite: 230.
Terms: Aut | Units: 1
Instructors: Jones, P.
BIO 231: Evolution of Life Histories
Life histories as descriptions of reproduction, survival, and growth over the lives of individuals. Theoretical approaches to the dynamics and evolution of life histories and of populations with different life histories. Experimental data on natural populations and methods for their analysis.
Terms: alternate years, given next year | Units: 3
BIO 232: Advanced Imaging Lab in Biophysics (APPPHYS 232, BIO 132, BIOPHYS 232, MCP 232)
Laboratory and lectures. Advanced microscopy and imaging, emphasizing hands-on experience with state-of-the-art techniques. Students construct and operate working apparatus. Topics include microscope optics, Koehler illumination, contrast-generating mechanisms (bright/dark field, fluorescence, phase contrast, differential interference contrast), and resolution limits. Laboratory topics vary by year, but include single-molecule fluorescence, fluorescence resonance energy transfer, confocal microscopy, two-photon microscopy, and optical trapping. Limited enrollment. Recommended: basic physics, Biology core or equivalent, and consent of instructor.
Terms: Spr | Units: 4
Instructors: Block, S.; Schnitzer, M.; Smith, S.; Stearns, T.
BIO 237: Plant Genetics (BIO 137)
Gene analysis, mutagenesis, transposable elements; developmental genetics of flowering and embryo development; biochemical genetics of plant metabolism; scientific and societal lessons from transgenic plants. Prerequisite: Biology core or consent of instructor.
Terms: Spr | Units: 3-4
Instructors: Walbot, V.
BIO 243: Evolution (BIO 143)
The basic facts and principles of the evolution of all life. The logic of and evidence for the correctness of Darwin's argument for evolution by natural selection. How Mendelian genetics was integrated into evolutionary thinking. The integration of physiological and ecological perspectives into the study of evolutionary adaptation within species. Species formation and evolutionary divergence among species. Patterns of evolution over long time scales.
Terms: Aut | Units: 3
Instructors: Watt, W.
BIO 244: Fundamentals of Molecular Evolution (BIO 113)
The inference of key molecular evolutionary processes from DNA and protein sequences. Topics include random genetic drift, coalescent models, effects and tests of natural selection, combined effects of linkage and natural selection, codon bias and genome evolution. Prerequisites: Biology core or graduate standing in any department, and consent of instructor.
Terms: Spr | Units: 4
Instructors: Petrov, D.
BIO 245: Behavioral Ecology (BIO 145)
Animal behavior from an evolutionary and ecological perspective. Topics: foraging, territoriality, reproductive behavior, social groups. Lecture/seminar format; seminars include discussion of journal articles. Independent research projects. Prerequisites: Biology or Human Biology core, or consent of instructor. Recommended: statistics.
Terms: not given this year | Units: 4
BIO 247: Controlling Climate Change in the 21st Century (BIO 147, EARTHSYS 147, EARTHSYS 247, HUMBIO 116)
Global climate change science, impacts, and response strategies. Topics: scientific understanding of the climate system; modeling future climate change; global and regional climate impacts and vulnerability; mitigation and adaptation approaches; the international climate policy challenge; and decarbonization of energy and transportation systems.
Terms: alternate years, given next year | Units: 3
BIO 249: The Neurobiology of Sleep (BIO 149, HUMBIO 161)
(Graduate students register for 249.) Preference to seniors and graduate students. The neurochemistry and neurophysiology of changes in brain activity and conscious awareness associated with changes in the sleep/wake state. Behavioral and neurobiological phenomena including sleep regulation, sleep homeostasis, circadian rhythms, sleep disorders, sleep function, and the molecular biology of sleep. Enrollment limited to 16.
Terms: alternate years, given next year | Units: 4
BIO 250: Human Behavioral Biology (BIO 150, HUMBIO 160)
Multidisciplinary. How to approach complex normal and abnormal behaviors through biology. How to integrate disciplines including sociobiology, ethology, neuroscience, and endocrinology to examine behaviors such as aggression, sexual behavior, language use, and mental illness.
Terms: Spr, alternate years, not given next year | Units: 5
Instructors: Sapolsky, R.
BIO 254: Molecular and Cellular Neurobiology (BIO 154, NBIO 254)
For advanced undergraduates and graduate students. Cellular and molecular mechanisms in the organization and functions of the nervous system. Topics: wiring of the neuronal circuit, synapse structure and synaptic transmission, signal transduction in the nervous system, sensory systems, molecular basis of behavior including learning and memory, molecular pathogenesis of neurological diseases. Prerequisite for undergraduates: Biology core or equivalent, or consent of instructors.
Terms: alternate years, given next year | Units: 4-5
BIO 256: Epigenetics (BIO 156, GENE 206, PATH 206)
For graduate students in the Biosciences and upper level Biology undergraduates. Mechanisms by which phenotypes not determined by the DNA sequence are stably inherited in successive cell divisions. From the discovery of position-effect variegation in Drosophila in the 1920s to present-day studies of covalent modifications of histones and DNA methylation. Topics include: position effect, gene silencing, heterochromatin, centromere identity, genomic imprinting, histone code, variant histones, and the role of epigenetics in cancer. Prerequisite: BIO41 and BIO42 , or GENE 203, or consent of instructor.
Terms: Spr, alternate years, not given next year | Units: 2
Instructors: Gozani, O.; Lipsick, J.
BIO 257: Plant Biochemistry (BIO 157)
The biochemistry of plants relevant to their physiology and cell biology. Topics include: the biosynthesis, assembly, function, and regulation of cell walls; lipids; pigments; photoreceptors; transporters; and the response of plants to pathogens and stresses. Prerequisite: Biology core or equivalent, or consent of instructors.
Terms: not given this year | Units: 3-4
BIO 258: Neural Development
For Ph.D. students. Seminar; students also attend BIO 158 lectures. Topics: neural induction and patterning, cell lineage, neurogenesis, neuronal migration, axonal pathfinding, synapse elimination, the role of activity, critical periods, and the development of behavior.
Terms: alternate years, given next year | Units: 4
BIO 263: Neural Systems and Behavior (BIO 163, HUMBIO 163)
The field of neuroethology and its vertebrate and invertebrate model systems. Research-oriented. Readings include reviews and original papers. How animal brains compare; how neural circuits are adapted to species-typical behavior; and how the sensory worlds of different species represent the world. Lectures and required discussions. Prerequisites: BIO 42, HUMBIO 4A.
Terms: Aut, alternate years, given next year | Units: 4
Instructors: Fernald, R.
BIO 264: Biosphere-Atmosphere Interactions (BIO 164)
Physiological, ecological, and physical aspects of ecosystem function, emphasizing how ecosystems influence and are influenced by the atmosphere. Prerequisites: 42, 43; or consent of instructor.
Terms: alternate years, given next year | Units: 4
BIO 265: Cellular and Molecular Therapeutic Approaches to Neurological Disorders (BIO 165)
Current therapeutic research for neurological conditions, including stroke, epilepsy, neurodegenerative disorders, depression, anxiety, and aging. Sources include primary literature. Guest lecturers.
Terms: Win | Units: 1
Instructors: Sorrells, S.
BIO 266: Faunal Analysis: Animal Remains for the Archaeologist (ANTHRO 113, ANTHRO 213, BIO 166)
The analysis of fossil animal bones and shells to illuminate the behavior and ecology of prehistoric collectors, especially ancient humans. Theoretical and methodoloigcal issues. The identification, counting, and measuring of fossil bones and shells. Labs. Methods of numerical analysis.
Terms: not given this year | Units: 5
BIO 267: Molecular Mechanisms of Neurodegenerative Disease (NENS 267)
The epidemic of neurodegenerative disorders such as Alzheimer's and Parkinson's disease occasioned by an aging human population. Genetic, molecular, and cellular mechanisms. Clinical aspects through case presentations.
Terms: Win, alternate years, not given next year | Units: 4
Instructors: Kopito, R.; Reimer, R.; Wyss-Coray, A.
BIO 271: Principles of Cell Cycle Control (BIO 171)
Genetic analysis of the key regulatory circuits governing the control of cell division. Illustration of key principles that can be generalized to other synthetic and natural biological circuits. Focus on tractable model organisms; growth control; irreversible biochemical switches; chromosome duplication; mitosis; DNA damage checkpoints; MAPK pathway-cell cycle interface; oncogenesis. Analysis of classic and current primary literature.
Terms: Aut | Units: 3
Instructors: Skotheim, J.
BIO 274S: Hopkins Microbiology Course (BIOHOPK 274, CEE 274S, EESS 253S)
(Formerly GES 274S.) Four-week, intensive. The interplay between molecular, physiological, ecological, evolutionary, and geochemical processes that constitute, cause, and maintain microbial diversity. How to isolate key microorganisms driving marine biological and geochemical diversity, interpret culture-independent molecular characterization of microbial species, and predict causes and consequences. Laboratory component: what constitutes physiological and metabolic microbial diversity; how evolutionary and ecological processes diversify individual cells into physiologically heterogeneous populations; and the principles of interactions between individuals, their population, and other biological entities in a dynamically changing microbial ecosystem. Prerequisites: CEE 274A,B, or equivalents.
Terms: Sum | Units: 9-12 | Repeatable for credit
Instructors: Francis, C.; Spormann, A.
BIO 277: Plant Microbe Interaction (BIO 177)
Plant pathology and plant symbiosis.Topics include: prokaryotic and eukaryotic pathogens; molecular, genetic, and cellular basis for microbial pathogenicity and host defense; genetics and cell biology of nitrogen-fixing symbiosis and for mycorrhizal associations. Evolutionary context. Prerequisites: Biology core and two or more upper division courses in genetics, molecular biology, or biochemistry. Recommended: plant genetics or plant biochemistry.
Terms: Spr, alternate years, not given next year | Units: 3
Instructors: Long, S.; Mudgett, M.
BIO 278: Microbiology Literature (BIO 178)
Critical reading of the research literature in prokaryotic genetics and molecular biology, with particular applications to the study of major human pathogens. For advanced undergraduates and first or second year graduate students. Classic and foundational papers in pathogenesis, genetics, and molecular biology; more recent literature on prokaryotic pathogens such as Salmonella, Vibrio, and/or Yersinia. Current papers will cover research approaches including biochemistry, genomics, pathogenesis, and cell biology. Prerequisites: Biology Core and two upper-division courses in genetics, molecular biology, or biochemistry.
Terms: Win | Units: 3
Instructors: Long, S.
BIO 283: Theoretical Population Genetics (BIO 183)
Models in population genetics and evolution. Selection, random drift, gene linkage, migration, and inbreeding, and their influence on the evolution of gene frequencies and chromosome structure. Models are related to DNA sequence evolution. Prerequisites: calculus and linear algebra, or consent of instructor.
Terms: Spr | Units: 3
Instructors: Feldman, M.
BIO 285: Evolution of Reproductive Social Behavior (BIO 185)
Seminar. Controversies surrounding theory and data for the evolution of sex, gender, and sexuality. Issues include the critique of Darwin's theory of sexual selection, and the accuracy of the metaphor of universal selfishness and sexual conflict in biological nature. Readings include Evolution's Rainbow and The Genial Gene, and primary literature.
Terms: Aut | Units: 3
Instructors: Roughgarden, J.
BIO 286: Natural History of the Vertebrates (BIO 186)
Broad survey of the diversity of vertebrate life. Discussion of the major branches of the vertebrate evolutionary tree, with emphasis on evolutionary relationships and key adaptations as revealed by the fossil record and modern phylogenetics. Modern orders introduced through an emphasis on natural history, physiology, behavioral ecology, community ecology, and conservation. Lab sessions focused on comparative skeletal morphology through hands-on work with skeletal specimens. Discussion of field methods and experience with our local vertebrate communities through field trips to several of California¿s distinct biomes. Prerequisite: Biology core.
Terms: Spr, alternate years, not given next year | Units: 4
Instructors: Hadly, E.
BIO 288: Biochemistry I (BIO 188, CHEM 181, CHEMENG 181, CHEMENG 281)
(CHEMENG offerings formerly listed as 188/288.) Chemistry of major families of biomolecules including proteins, nucleic acids, carbohydrates, lipids, and cofactors. Structural and mechanistic analysis of properties of proteins including molecular recognition, catalysis, signal transduction, membrane transport, and harvesting of energy from light. Molecular evolution. Prerequisites: CHEM 135 or 171.
Terms: Win | Units: 3
Instructors: Cegelski, L.; Zare, R.
BIO 289: Biochemistry II (BIO 189, CHEM 183, CHEMENG 183, CHEMENG 283)
Focus on metabolic biochemistry: the study of chemical reactions that provide the cell with the energy and raw materials necessary for life. Topics include glycolysis, gluconeogenesis, the citric acid cycle, oxidative phosphorylation, photosynthesis, the pentose phosphate pathway, and the metabolism of glycogen, fatty acids, amino acids, and nucleotides as well as the macromolecular machines that synthesize RNA, DNA, and proteins. Medical relevance is emphasized throughout. Prerequisite: BIO 188/288 or CHEM 181 or CHEMENG 181/281 (formerly 188/288).
Terms: Spr | Units: 3
Instructors: Dunn, A.
BIO 290: Teaching of Biology
Open to upper-division undergraduates and graduate students. Practical experience in teaching lab biology or serving as an assistant in a lecture course. May be repeated for credit. Prerequisite: consent of instructor.
Terms: Aut, Win, Spr | Units: 1-5
Instructors: Baker, B.; Barton, K.; Bergmann, D.; Berry, J.; Block, B.; Block, S.; Boggs, C.; Burkholder, W.; Campbell, A.; Cyert, M.; Daily, G.; Denny, M.; Dirzo, R.; Ehrlich, P.; Epel, D.; Fang, G.; Feldman, M.; Fernald, R.; Field, C.; Frommer, W.; Frydman, J.; Fukami, T.; Gilly, W.; Gordon, D.; Gozani, O.; Green, E.; Grossman, A.; Hadly, E.; Hanawalt, P.; Heller, H.; Jones, P.; Khalfan, W.; Klein, R.; Kopito, R.; Long, S.; Luo, L.; Malladi, S.; McConnell, S.; Micheli, F.; Mooney, H.; Mudgett, M.; Nelson, W.; Palumbi, S.; Petrov, D.; Root, T.; Roughgarden, J.; Sapolsky, R.; Schneider, S.; Schnitzer, M.; Shen, K.; Simon, M.; Simoni, R.; Skotheim, J.; Somero, G.; Somerville, C.; Spormann, A.; Stearns, T.; Thompson, S.; Tuljapurkar, S.; Vitousek, P.; Walbot, V.; Wang, Z.; Watanabe, J.; Watt, W.; Weissman, I.
BIO 290X: Out-of-Department Teaching
May be repeated for credit. Prerequisite: consent of instructor.
Terms: Aut, Win, Spr | Units: 1-5
Instructors: Garza, D.; Khosla, C.
BIO 291: Development and Teaching of Core Experimental Laboratories
Preparation for teaching the core experimental courses (44X and 44Y). Emphasis is on lab, speaking, and writing skills. Focus is on updating the lab to meet the changing technical needs of the students. Must be taken prior to teaching either of the above courses. May be repeated for credit. Prerequisite: selection by instructor.
Terms: Aut, Win | Units: 1-2
Instructors: Malladi, S.
BIO 294: Cellular Biophysics (APPPHYS 294)
Physical biology of dynamical and mechanical processes in cells. Emphasis is on qualitative understanding of biological functions through quantitative analysis and simple mathematical models. Sensory transduction, signaling, adaptation, switches, molecular motors, actin and microtubules, motility, and circadian clocks. Prerequisites: differential equations and introductory statistical mechanics.
Terms: Aut, alternate years, not given next year | Units: 3
Instructors: Fisher, D.
BIO 300: Graduate Research
For graduate students only. Individual research by arrangement with in-department instructors.
Terms: Aut, Win, Spr, Sum | Units: 1-15
Instructors: Baker, B.; Barton, K.; Bergmann, D.; Berry, J.; Block, B.; Block, S.; Boggs, C.; Burkholder, W.; Campbell, A.; Cyert, M.; Daily, G.; Denny, M.; Dirzo, R.; Ehrlich, P.; Epel, D.; Fang, G.; Feldman, M.; Fernald, R.; Field, C.; Frommer, W.; Frydman, J.; Fukami, T.; Gilly, W.; Gordon, D.; Gozani, O.; Grossman, A.; Hadly, E.; Hanawalt, P.; Heller, H.; Jones, P.; Klein, R.; Kopito, R.; Long, S.; Luo, L.; McConnell, S.; Micheli, F.; Mooney, H.; Mudgett, M.; Nelson, W.; Palumbi, S.; Petrov, D.; Root, T.; Roughgarden, J.; Sapolsky, R.; Schneider, S.; Schnitzer, M.; Shen, K.; Simon, M.; Simoni, R.; Skotheim, J.; Somero, G.; Somerville, C.; Spormann, A.; Stearns, T.; Thompson, S.; Tuljapurkar, S.; Vitousek, P.; Walbot, V.; Wang, Z.; Watt, W.; Weissman, I.
BIO 300X: Out-of-Department Graduate Research
Individual research by arrangement with out-of-department instructors. Master's students: credit for work arranged with out-of-department instructors is restricted to Biology students and requires approved department petition. See http://biohonors.stanford.edu for more information. May be repeated for credit.
Terms: Aut, Win, Spr, Sum | Units: 1-15
Instructors: Andriacchi, T.; Barres, B.; Behr, B.; Bergmann, D.; Blau, H.; Block, B.; Block, S.; Boggs, C.; Boothroyd, J.; Brown, P.; Brunet, A.; Brunger, A.; Burgos, A.; Burkholder, W.; Campbell, A.; Chen, J.; Cimprich, K.; Clandinin, T.; Cleary, M.; Cochran, J.; Contag, C.; Crabtree, G.; Cyert, M.; Daily, G.; Davis, M.; Davis, R.; Denny, M.; Dirzo, R.; Ehrhardt, D.; Ehrlich, P.; Epel, D.; Fathman, C.; Feldman, M.; Felsher, D.; Fernald, R.; Field, C.; Fire, A.; Ford, J.; Fredericson, M.; Freyberg, D.; Frydman, J.; Fukami, T.; Fuller, M.; Gardner, C.; Garner, C.; Gilly, W.; Glenn, J.; Gold, G.; Goodman, M.; Goodman, S.; Gordon, D.; Gozani, O.; Hadly, E.; Hanawalt, P.; Haskell, W.; Heilshorn, S.; Heller, H.; Helms, J.; Herzenberg, L.; Hsu, S.; Jones, P.; Katzenstein, D.; Kay, M.; Kim, S.; Koong, A.; Kopito, R.; Kornberg, A.; Krams, S.; Kuo, C.; Launer, A.; Lee, P.; Levy, R.; Long, S.; Longaker, M.; Luo, L.; Lyons, D.; MacIver, M.; Maduke, M.; Marinkovich, M.; Matheson, G.; McConnell, S.; Micheli, F.; Mignot, E.; Miklos, D.; Mochly-Rosen, D.; Monack, D.; Mooney, H.; Morris, R.; Mudgett, M.; Murphy, G.; Nadeau, K.; Naumovski, L.; Nayak, N.; Nelson, W.; Nishino, S.; Nolan, G.; Nusse, R.; Palmer, T.; Palumbi, S.; Parker, K.; Petrov, D.; Pollack, J.; Pringle, J.; Raymond, J.; Reimer, R.; Relman, D.; Robinson, W.; Rockson, S.; Rothschild, L.; Roughgarden, J.; Sage, J.; Sapolsky, R.; Schneider, S.; Schnitzer, M.; Scott, M.; Shapiro, L.; Shen, K.; Shooter, E.; Shulman, N.; Sibley, E.; Sikic, B.; Simon, M.; Simoni, R.; Singh, U.; Skirboll, S.; Skotheim, J.; Somero, G.; Spormann, A.; Spudich, J.; Stearns, T.; Steinman, L.; Sun, Z.; Sweet-Cordero, E.; Tan, M.; Thompson, S.; Triadafilopoulos, G.; Tuljapurkar, S.; Umetsu, D.; Vemuri, M.; Vitousek, P.; Walbot, V.; Watt, W.; West, R.; Wong, A.; Wu, J.; Yang, Y.; Yao, M.; Zarins, C.; Zhao, H.; de Lecea, L.
BIO 301: Frontiers in Biology
Limited to and required of first-year Ph.D. students in molecular, cellular, and developmental biology. Current research in molecular, cellular, and developmental biology emphasizing primary research literature. Held in conjunction with the department's Monday seminar series. Students and faculty meet weekly before the seminar for a student presentation and discussion of upcoming papers.
Terms: Aut, Win | Units: 1-
Instructors: Morrison, A.; Skotheim, J.
BIO 302: Current Topics and Concepts in Population Biology, Ecology, and Evolution
Required of first-year PhD students in population biology, and ecology and evolution. Major conceptual issues and developing topics.
Terms: Aut | Units: 1
Instructors: Ehrlich, P.
BIO 303: Current Topics and Concepts in Population Biology, Ecology, and Evolution
Required of first-year PhD students in population biology, and ecology and evolution. Major conceptual issues and developing topics.
Terms: Win | Units: 1
Instructors: Ehrlich, P.
BIO 304: Current Topics and Concepts in Population Biology, Ecology, and Evolution
Required of first-year PhD students in population biology, and ecology and evolution. Major conceptual issues and developing topics.
Terms: Spr | Units: 1
Instructors: Ehrlich, P.
BIO 306: Current Topics in Integrative Organismal Biology
Limited to and required of graduate students doing research in this field. At Hopkins Marine Station.
Terms: Aut | Units: 1
Instructors: Fernald, R.; Heller, H.; Sapolsky, R.
BIO 312: Ethical Issues in Ecology and Evolutionary Biology
Focus is on ethical issues addressed in Donald Kennedy's Academic Duty and others of importance to academics and scientists in the fields of ecology, behavior, and evolutionary biology. Discussions led by faculty and outside guests. Satisfies ethics course requirement for ecology and evolutionary biology. Prerequisite: PhD student in the ecology and evolutionary biology or marine program, or consent of instructor.
Terms: Aut | Units: 1
Instructors: Ehrlich, P.
BIO 315: Seminar in Biochemical Evolution
Literature review and discussion of current topics in biochemical evolution and molecular evolutionary genetics. Prerequisite: consent of instructor.
Terms: Aut, Win, Spr | Units: 1-3
Instructors: Watt, W.
BIO 323: Detecting Climate-Driven Changes in California Plant Ranges
Seminar. For advanced undergraduates and graduate students. Future anthropogenic climate change will continue to alter plant communities, plant ranges, and ecosystems. Studies have already documented plant and animal range shifts across the globe, yet many questions remain as to how plants will respond to climate change. Which taxa and functional groups will be most sensitive to changes in climate? What will happen to ecological communities with differential response of plant species to climate? Focus is on analyzing trends in climate change and long-term plant distribution data in California. May be repeated for credit. Prerequisite: familiarity with statistical, spatial, or modeling analyses.
Terms: not given this year | Units: 1-2
BIO 324: Interpreting Ecological Data
Experimental design and the theory behind and appropriate use of parametric statistics including: student t-test; analysis of variance; linear regression and some variations including logistic regression and multiple regression; analysis of covariance; chi-squared similarity test; testing the independence of multiple tests; Monte Carlo and bootstrapping methods. Students encouraged to use data from their own research. Course does not fulfill undergraduate statistics requirement. Prerequisite: consent of instructor.
Terms: not given this year | Units: 4
BIO 325: The Evolution of Body Size (GES 325)
The influence of organism size on evolutionary and ecological patterns and processes. Focus is on integration of theoretical principles, observations of living organisms, and data from the fossil record. What are the physiological and ecological correlates of body size? Is there an optimum size? Do organisms tend to evolve to larger size? Does productivity control the size distribution of consumers? Does size affect the likelihood of extinction or speciation? How does size scale from the genome to the phenotype? How is metabolic rate involved in evolution of body size? What is the influence of geographic area on maximum body size?
Terms: not given this year | Units: 2
BIO 326: Foundations in Biogeography
Seminar. Focus on classic papers covering the global distribution and abundance of organisms through time. Topics include: phylogenetics, phylogeography, plate tectonics, island biogeography, climatic change, dispersal, vicariance, ecology of invasions, extinction, gradients, diversity, conservation and a history of the field.
Terms: Win, alternate years, not given next year | Units: 2
Instructors: Fukami, T.; Hadly, E.
BIO 342: Plant Biology Seminar
Topics announced at the beginning of each quarter. Current literature. May be repeated for credit. See http://carnegiedpb.stanford.edu/seminars/seminars.php.
Terms: Aut, Win, Spr | Units: 1
Instructors: Walbot, V.
BIO 344: Advanced Seminar in Cellular Biology
Enrollment limited to graduate students directly associated with departmental research groups working in cell biology.
Terms: not given this year | Units: 1
BIO 346: Advanced Seminar on Prokaryotic Molecular Biology
Enrollment limited to PhD students associated with departmental research groups in genetics or molecular biology.
Terms: not given this year | Units: 1
BIO 383: Seminar in Population Genetics
Literature review, research, and current problems in the theory and practice of population genetics and molecular evolution. Prerequisite: consent of instructor.
Terms: Aut, Win, Spr | Units: 1-3
Instructors: Feldman, M.
BIO 384: Theoretical Ecology
Recent and classical research papers in ecology, and presentation of work in progress by participants. Prerequisite: consent of instructor.
Terms: not given this year | Units: 1-3
BIO 388: Communication and Leadership Skills (IPER 210)
Focus is on delivering information to policy makers and the lay public. How to speak to the media, Congress, and the general public; how to write op-eds and articles; how to package ideas including titles, abstracts, and CVs; how to survive peer review, the promotion process, and give a job talk; and how to be a responsible science advocate.
Terms: Spr | Units: 2
BIO 459: Frontiers in Interdisciplinary Biosciences (BIOC 459, BIOE 459, CHEM 459, CHEMENG 459, PSYCH 459)
Students register through their affiliated department; otherwise register for CHEMENG 459. For specialists and non-specialists. Sponsored by the Stanford BioX Program. Three seminars per quarter address scientific and technical themes related to interdisciplinary approaches in bioengineering, medicine, and the chemical, physical, and biological sciences. Leading investigators from Stanford and the world present breakthroughs and endeavors that cut across core disciplines. Pre-seminars introduce basic concepts and background for non-experts. Registered students attend all pre-seminars; others welcome. See http://biox.stanford.edu/courses/459.html. Recommended: basic mathematics, biology, chemistry, and physics.
Terms: Aut, Win, Spr | Units: 1
Instructors: Robertson, C.