BIO 1:
Human Evolution and Environment
Human genetic and cultural evolution and how people interact with their environments, from the ancestors of Australopithecus to current events. Issues include race, gender, and intelligence; pesticide and antibiotic resistance; abortion and contraception; ecosystem services; environmental economics and ethics; the evolution of religion; climate change; population growth and overconsumption; origins and spread of ideas and technologies; and the distribution of political and economic power.
Terms: Spr
| Units: 3
| UG Reqs: GER: DB-NatSci
BIO 3:
Frontiers in Marine Biology
An introduction to contemporary research in marine biology, including ecology, conservation biology, environmental toxicology, behavior, biomechanics, evolution, neurobiology, and molecular biology. Emphasis is on new discoveries and the technologies used to make them. Weekly lectures by faculty from the Hopkins Marine Station.
Terms: Aut
| Units: 1
BIO 3N:
Views of a Changing Sea: Literature & Science
The state of a changing world ocean, particularly in the eastern Pacific, will be examined through historical and contemporary fiction, non-fiction and scientific publications. Issues will include harvest and mariculture fisheries, land-sea interactions and oceanic climate change in both surface and deep waters.
| Units: 3
| UG Reqs: GER: DB-NatSci
BIO 7N:
Introduction to Conservation Photography
Introduction to the field of conservation photography and the strategic use of visual communication in addressing issues concerning the environment and conservation. Students will be introduced to basic digital photography, digital image processing, and the theory and application of photographic techniques. Case studies of conservation issues will be examined through photographs and multimedia platforms including images, video, and audio. Lectures, tutorials, demonstrations, and mandatory field trips will culminate in the production of individual and group projects.
Terms: Win
| Units: 3
| UG Reqs: WAY-CE
BIO 7S:
Introduction to Biology
The major fields of biology: biochemistry, the cell, evolution, and diversity. Foundation for higher-level biology courses.
Terms: Sum
| Units: 3
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 7SL:
Introduction to Biology Lab
Optional lab to be taken concurrently with BIO 7S.
Terms: Sum
| Units: 2
BIO 9S:
Introduction to Biological Research Methods
Theory and practice of experimental biology. Introduction to how to plan an experiment, conduct, and analyze data. Introduction to scientific writing and reading scientific journal articles. Prerequisite: high school biology.
Last offered: Summer 2011
| Units: 3
| UG Reqs: GER: DB-NatSci
BIO 10SC:
Natural History, Marine Biology, and Research
Monterey Bay is home to the nation's largest marine sanctuary and also home to Stanford¿s Hopkins Marine Station. This course, based at Hopkins, explores the spectacular biology of Monterey Bay and the artistic and political history of the region. The course focuses on issues of conservation, sanctuary, and stewardship of the oceans and coastal lands. We will meet with conservationists, filmmakers, artists, authors, environmentalists, politicians, land-use planners, and lawyers, as well as scientists and educators, to learn what is being done to appreciate, protect, and study the coastline and near-shore waters at local and national levels. We will take a look at the discipline of marine biology to discover the range of topics and methods of research it embraces and to help define some of the larger issues in biology that loom in our future. The course emphasizes interactions and discussions between individuals, groups, and our guests; it is a total immersion experience. We will be together all of the time, either at our base at the Belden House in Pacific Grove or hiking and camping in Big Sur.nnStudents are expected to have read the several books provided as introductory material before the course begins, and each is also expected to become our local expert in an area such as plant identification, bird identification, poetry, weather prediction, photography, history, ethnography, etc. The course requires an individual research project of your choice on a topic related to the general theme. Final reports will be presented at the last meeting of the group and may involve any medium, including written, oral, and performance media.nnNote: This course will be held at the Hopkins Marine Station in the Monterey region, and housing will be provided nearby. Transportation from campus to the housing site will be provided once students arrive on campus on August 30. Transportation to campus from the Belden House in Pacific Grove will be provided on September 19. Sophomore College Course: Application required, due noon, April 7, 2015. Apply at http://soco.stanford.edu
Terms: Sum
| Units: 2
BIO 11N:
Biotechnology in Everyday Life
Preference to freshmen. The science that makes transgenic plants and animals possible. Current and future applications of biotechnology and the ethical issues raised.
Terms: Aut
| Units: 3
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 12N:
Sensory Ecology of Marine Animals
Animals living in the oceans experience a highly varied range of environmental stimuli. An aquatic lifestyle requires an equally rich range of sensory adaptations, including some that are totally foreign to us. In this course we will examine sensory system in marine animals from both an environmental and behavioral perspective and from the point of view of neuroscience and information systems engineering.
Terms: Aut
| Units: 3
| UG Reqs: WAY-SMA
BIO 15N:
Environmental Literacy
Preference to freshmen. Lack of public understanding of the details of most environmental problems is cited as a cause of environmental deterioration. Good citizenship requires literacy about the elements of the scientific and decision making processes that accompany most environmental issues: what can happen, what are the odds, how can the credibility of sources of expertise be assessed, which components of environmental debates deal with factual and theoretical issues, and which are political value judgments?
Terms: Aut
| Units: 3
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 17N:
Getting Renewable Energy up to Scale: The Problem of Location
As the climate continues to warm, plants and animals around the globe have a higher risk of going extinct. The Intergovernmental Panel for Climate Change (IPCC) Assessment Report 4 said in 2007 that when the global average temperature gets to 2 degrees C (3.6 degrees F) above the global average temperature in the mid 1700s, 20 to 40% of the species on the plant could be at high risk of extinction. Given that we know about two million species on the planet that means that 400,000 to 800,000 species could be at high risk. The IPCC went on to say that if the global average temperature gets to as much as 4 degrees C (7.2 degrees F) above natural, then as many as half of the species on the plant could be at high risk of extinction. Currently we are on a trajectory of surpassing 2 degrees C well before the end of the 21st Century. The only way to drop to a lower temperature trajectory is to decrease the amount of CO2 in the atmosphere, which can be done by either scrubbing the CO2 out of the atmosphere or decreasing our emission of CO2. Techniques to do the former at the scale needed are not known as of yet, while decreasing our emissions substantially we do understand: it will require increasing substantially the amount of renewable energy used, which in turn will require deployment of renewables to a much greater amount than is planned currently. One of the main reasons holding up deployment of renewables is the debate about where the renewables will be located. This seminar will examine the arguments about the need for renewables, investigate the pros and cons of locating renewable at different sites and try to determine if and where the best locations might be.
Terms: Spr
| Units: 3
BIO 22Q:
Infection, Immunity, and Global Health
Why do infectious diseases continue to challenge us despite advances in medicine? This course will explore the causes and prevention of infectious diseases, focusing on the interplay between pathogens, the immune system, the environment, and societal factors that affect disease occurrence and outcomes. Topics will include: basic elements of microbiology, immunology, and epidemiology; case studies of old diseases (e.g., smallpox, tuberculosis, malaria) and recently-emergent diseases (e.g., Ebola, AIDS, antibiotic-resistant bacteria, Lyme disease, and pandemic influenza) that illustrate the biological, environmental, cultural, political, and economic factors that affect disease emergence, spread, and control; the limitations of modern medical approaches such as antibiotics and vaccines; and strategies for reducing global infectious disease threats. The seminar will feature class discussion, student projects, and faculty and student presentations. Prerequisite: biology background, preferably introductory college courses (e.g., 41, 42, or HUMBIO 2A, 3A).
Terms: Spr
| Units: 3
| UG Reqs: GER: DB-NatSci
BIO 26N:
Maintenance of the Genome
Preference to freshmen. The precious blueprint for life is entrusted to the genomic DNA molecules in all living cells. Multiple strategies have evolved to prevent the deleterious consequences from endogenous DNA alterations and damage from radiation or genotoxic chemicals in the environment. In this seminar you will learn about the remarkable systems that scan cellular DNA for alterations and make repairs to ensure genomic stability. Deficiencies in DNA repair have been implicated in many hereditary diseases involving developmental defects, premature aging, and/or predisposition to cancer. An understanding of DNA repair mechanisms is important for advances in the fields of cancer biology, neurobiology, and gerontology. Background readings, introductory lectures, student presentations, short term paper.
Terms: Aut
| Units: 3
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 30:
Ecology for Everyone (EARTHSYS 30)
Everything is connected, but how? Ecology is the science of interactions and the changes they generate. This project-based course links individual behavior, population growth, species interactions, and ecosystem function. Introduction to measurement, observation, experimental design and hypothesis testing in field projects, mostly done in groups. The goal is to learn to think analytically about everyday ecological processes involving bacteria, fungi, plants, animals and humans. The course uses basic statistics to analyze data; there are no math prerequisites except arithmetic. Open to everyone, including those who may be headed for more advanced courses in ecology and environmental science.
Terms: Spr
| Units: 4
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 30N:
Extinctions in Near Time: Biodiversity loss since the Pleistocene
The transition 11,700 years ago from the Pleistocene glacial period into the Holocene interglacial witnessed the expansion of humans around the world, climatic warming and the demise of many large vertebrate species. Since that time extinctions have continued on land and in the sea, culminating with the biodiversity crisis we are experiencing today. We will explore these prehistoric extinctions: "Who? When? Where? and Why?" in order to learn more about our planet's future.
Last offered: Autumn 2012
| Units: 3
| UG Reqs: GER: DB-NatSci, WAY-CE, WAY-SMA
BIO 33N:
Conservation Science and Practice
Preference to freshmen. Interdisciplinary. The science and art of conservation today. The forces that are driving change in Earth's atmosphere, lands, waters, and variety of life forms. Which broad dimensions of the biosphere, and which elements of ecosystems, most merit protection? The prospects for, and challenges in, making conservation economically attractive and commonplace. Field trip; project.
Last offered: Spring 2012
| Units: 3
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 34N:
Hunger
The biology of hunger and satiety, disease states that disrupt normal responses to hunger and satiety, starvation responses and adaptations to starvation in a variety of organisms, food production and distribution mechanisms, historic famines and their causes, the challenges of providing adequate food and energy for the Earth's growing population, local and global efforts to alleviate hunger, and hunger in fiction.
Terms: Aut
| Units: 3
| UG Reqs: GER: DB-NatSci
BIO 41:
Genetics, Biochemistry, and Molecular Biology
Emphasis is on macromolecules (proteins, lipids, carbohydrates, and nucleic acids) and how their structure relates to function and higher order assembly; molecular biology, genome structure and dynamics, gene expression from transcription to translation. Prerequisites: CHEM 31X (or 31A,B), 33. Recommended: CHEM 35; MATH 19, 20, 21 or 41, 42.
Terms: Aut
| Units: 5
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 41S:
Biochemistry, Genetics, and Molecular Biology
Emphasis is on macromolecules (proteins, lipids, carbohydrates, and nucleic acids) and how their structure relates to function and higher order assembly; molecular biology, genome structure and dynamics, gene expression from transcription to translation. Prerequisites: CHEM 31X (or 31A,B), 33; MATH 19, 20, 21 or 41, 42. Recommended: CHEM 35.
Last offered: Summer 2013
| Units: 5
| UG Reqs: GER: DB-NatSci
BIO 42:
Cell Biology and Animal Physiology
Cell structure and function; principles of animal physiology (immunology, renal, cardiovascular, sensory, motor physiology, and endocrinology); neurobiology from cellular basis to neural regulation of physiology. Prerequisites: CHEM 31X (or 31A,B), 33. Recommended: BIO 41; CHEM 35; MATH 19, 20, 21 or 41, 42.
Terms: Win
| Units: 5
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 43:
Plant Biology, Evolution, and Ecology
Principles of evolution: macro- and microevolution and population genetics. Ecology: the principles underlying the exchanges of mass and energy between organisms and their environments; population, community, and ecosystem ecology; populations, evolution, and global change. Equivalent to BIOHOPK 43. Prerequisites: CHEM 31X (or 31A,B), 33. Recommended: BIO 41, 42; CHEM 35; MATH 19, 20, 21 or 41, 42.
Terms: Spr
| Units: 5
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 44X:
Core Molecular Biology Laboratory
Investigate yeast strains that are engineered to express the human protein, p53, and use modern molecular methods to identify the functional consequences of p53 mutations isolated from tumor cells. Learn about the protein's role as a tumor suppressor through lectures and by reading and discussing journal articles. Use molecular visualization programs to examine the structure of wild type and mutant p53 proteins. Formulate a testable hypothesis and assay the ability of mutant p53 to direct expression of several reporter genes. During guided reflection, formulate further analyses to determine whether mutant p53 is present in the cell, can bind to DNA, and/or can enter the nucleus. Conduct lab experiments, present findings through a team oral presentation, as well as a scientific poster. Prerequisites: CHEM 31X, or 31A,B, and 33; concurrent or past enrollment in Biology or Human Biology core. 44X,Y should be taken sequentially in the same year, preferably as sophomores, to prepare for internships. Preference given to juniors and seniors in fall quarter, preference given to sophomores in winter quarter. Lab fee. Information about this class is available at http://bio44.stanford.edu.
Terms: Aut, Win
| Units: 5
| UG Reqs: WAY-SMA
Instructors: ;
Cyert, M. (PI);
Hekmat-Scafe, D. (PI);
Imam, J. (PI);
Malladi, S. (PI);
Stearns, T. (PI);
Beckwith, S. (TA);
Chandler-Brown, D. (TA);
Chung, J. (TA);
Conlon, M. (TA);
Garcia, M. (TA);
Kim, R. (TA);
Liu, B. (TA);
Robbins, N. (TA);
Simmons, A. (TA);
Su, T. (TA);
Torrez Dulgeroff, L. (TA);
Yang, Z. (TA)
BIO 44Y:
Core Plant Biology & Eco Evo Laboratory
The goal of this course is to develop an understanding of how to conduct biological research, using a topic in Ecology, Evolutionary Biology, and Plant Biology as a practical example. This includes the complete scientific process: assessing background literature, generating testable hypotheses, learning techniques for field- and lab-based data collection, analyzing data using appropriate statistical methods, and finally writing and sharing results. To build these skills, this course will focus on communities of microorganisms living in floral nectar at Stanford's nearby Jasper Ridge Biological Preserve. Students, working in teams, will develop novel research hypotheses and execute the necessary experiments and measurements to test these hypotheses. The capstone of the course will be an oral defense of students' findings, as well as a research paper in the style of a peer-reviewed journal article. Labs will be completed both on campus and at Jasper Ridge. Lab fee. Information about this class is available at http://bio44.stanford.edu.
Terms: Spr
| Units: 5
| UG Reqs: WAY-SMA
Instructors: ;
Fukami, T. (PI);
Hekmat-Scafe, D. (PI);
Kurten, E. (PI);
Malladi, S. (PI);
Arbisser, I. (TA);
Blair, L. (TA);
Bogar, L. (TA);
Kang, J. (TA);
Martin, J. (TA);
Russell, J. (TA)
BIO 101:
Ecology
The principles of ecology. Topics: interactions of organisms with their environment, dynamics of populations, species interactions, structure and dynamics of ecological communities, biodiversity. Half-day field trip required. Satisfies Central Menu Area 4. Prerequisite: 43, or consent of instructor. Recommended: statistics.
Terms: Aut
| Units: 4
| UG Reqs: GER: DB-NatSci
BIO 104:
Advanced Molecular Biology (BIO 200)
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. Satisfies Central Menu Area 1. Prerequisite: Biology core.
Terms: Win
| Units: 5
| UG Reqs: GER: DB-NatSci
BIO 105A:
Ecology and Natural History of Jasper Ridge Biological Preserve (EARTHSYS 105A)
Formerly 96A - Jasper Ridge Docent Training. First of two-quarter sequence training program to join the Jasper Ridge education/docent program. The scientific basis of ecological research in the context of a field station, hands-on field research, field ecology and the natural history of plants and animals, species interactions, archaeology, geology, hydrology, land management, multidisciplinary environmental education; and research projects, as well as management challenges of the preserve presented by faculty, local experts, and staff. Participants lead research-focused educational tours, assist with classes and research, and attend continuing education classes available to members of the JRBP community after the course.
Terms: Win
| Units: 4
BIO 105B:
Ecology and Natural History of Jasper Ridge Biological Preserve (EARTHSYS 105B)
Formerly 96B - Jasper Ridge Docent Training. First of two-quarter sequence training program to join the Jasper Ridge education/docent program. The scientific basis of ecological research in the context of a field station, hands-on field research, field ecology and the natural history of plants and animals, species interactions, archaeology, geology, hydrology, land management, multidisciplinary environmental education; and research projects, as well as management challenges of the preserve presented by faculty, local experts, and staff. Participants lead research-focused educational tours, assist with classes and research, and attend continuing education classes available to members of the JRBP community after the course.
Terms: Spr
| Units: 4
BIO 107:
Human Physiology Laboratory
This laboratory course is inquiry based, so the subject matter of the course will change in successive years. In 2013-14, the question to be researched will be, during exercise (physical work): "Is lactate a cause or consequence of muscle fatigue?" Students must be willing to participate both as experimenter and as subject, and be available for all discussion and lab sessions for the entire quarter. Since many experiments will involve exercise routines, students must be in good physical condition and sign a medical consent form. Prerequisite is Bio 42 or HumBio 4A. Satisfies WIM in biologynnCourse will be offered in Fall 2013 and Spring 2014. Enrollment for each course is limited to 16 students by application.
Terms: Aut, Spr
| Units: 4
BIO 108:
Essential Statistics for Human Biology (HUMBIO 85A)
Introduction to statistical concepts and methods that are essential to the study of questions in biology, environment, health, epidemiology and related areas. The course will teach and use the computer language R. Topics include distributions, probabilities, likelihood, linear models; illustrations will be based on recent research.
Terms: Spr
| Units: 4
| UG Reqs: WAY-AQR
BIO 109A:
The Human Genome and Disease (BIO 209A, BIOC 109A, BIOC 209A, 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. Students with a major, minor or coterm in Biology: 109A/209A or 109B/209B may count toward degree program but not both.
Terms: Win
| Units: 3
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 109B:
The Human Genome and Disease: Genetic Diversity and Personalized Medicine (BIO 209B, BIOC 109B, BIOC 209B)
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. Students with a major, minor or coterm in Biology: 109A/209A or 109B/209B may count toward degree program but not both.
Terms: Spr
| Units: 3
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 10AX:
Conservation Photography
Account of the genre of conservation photography and strategic use of visual communication in the environmental arena. Introduction to use of digital SLR cameras and digital image processing. Case studies of conservation issues accompanied by multimedia platforms including images, video, and audio. Theory and application of photographic techniques. Lectures, tutorials, demonstrations, and field trips. Individual and group projects.
| Units: 2
BIO 110:
DNA Replication and Genomic Maintenance (BIO 210)
Maintenance of the genome and its accurate replication are prerequisites for life. DNA replication is also intricately connected to pathways for responding to genotoxic stress, which include inevitable collisions with transcription. In eukaryotes, DNA repair and replication are tightly connected to chromatin modification. Emphasis for lecture topics include: DNA-templated chromatin transactions; Chromatin manipulation during replication and DNA damage responses; Structural biology and molecular mechanisms of replication and DNA repair enzymes; Inducible responses to genotoxic stress; Relationships of DNA damage processing to mutagenesis, carcinogenesis, aging and human genetic disease.
Terms: Spr
| Units: 3
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 112:
Human Physiology (BIO 212, HUMBIO 133)
Human physiology will be examined by organ systems: respiratory, cardiovascular, renal, and gastrointestinal. Concepts of cell and molecular biology that underlie organ development, pathophysiology and opportunities for regenerative medicine will be introduced. Signaling and integrative control by the endocrine, autonomic and central nervous systems will be introduced. Prerequisite: Biology or Human Biology core.
Terms: Win
| Units: 4
| UG Reqs: GER: DB-NatSci
BIO 113:
Fundamentals of Molecular Evolution (BIO 244)
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. Satisfies Central Menu Areas 1 or 4. Prerequisites: Biology core or graduate standing in any department, and consent of instructor.
Terms: Win
| Units: 4
| UG Reqs: GER: DB-NatSci
BIO 116:
Ecology of the Hawaiian Islands (EARTHSYS 116)
Terrestrial and marine ecology and conservation biology of the Hawaiian Archipelago. Taught in the field in Hawaii as part of quarter-long sequence of courses including Earth Sciences and Anthropology. Topics include ecological succession, plant-soil interactions, conservation biology, biological invasions and ecosystem consequences, and coral reef ecology. Restricted to students accepted into the Earth Systems of Hawaii Program.
Last offered: Autumn 2012
| Units: 4
| UG Reqs: GER: DB-NatSci
BIO 117:
Biology and Global Change (EARTHSYS 111, EESS 111)
The biological causes and consequences of anthropogenic and natural changes in the atmosphere, oceans, and terrestrial and freshwater ecosystems. Topics: glacial cycles and marine circulation, greenhouse gases and climate change, tropical deforestation and species extinctions, and human population growth and resource use. Prerequisite: Biology or Human Biology core or graduate standing.
Terms: Win
| Units: 4
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 118:
Genetic Analysis of Biological Processes (BIO 218)
Genetic principles and their experimental applications. Emphasis is on the identification and use of mutations to study cellular function. Satisfies Central Menu Areas 1 or 2. Prerequisite: Biology core.
Terms: Win
| Units: 4
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 120:
Bacteria in Health and Disease (MI 120)
Enrollment limited to junior and senior undergraduates, graduate students and medical students. Introduces students to the bacteria that live in and on humans and, in some cases, can cause disease and sometimes death. Topics include the biology of the interaction of the simple microbe with complex human biology and the factors that determine whether or not we coexist relatively peacefully, suffer from overt disease, or succumb to the bacterial onslaught.
Terms: Spr
| Units: 3
BIO 121:
Biogeography
Global distributions of organisms through the Phanerozoic, with emphasis on historical causes. Topics: plate tectonics, island biogeography, climatic change, dispersal, vicariance, ecology of invasions, extinction, gradients, diversity. Satisfies Central Menu Area 4.
Last offered: Spring 2009
| Units: 3
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 126:
Introduction to Biophysics (APPPHYS 205, BIO 226)
Core course appropriate for advanced undergraduate students and graduate students with prior knowledge of calculus and a college physics course. Introduction to how physical principles offer insights into modern biology, with regard to the structural, dynamical, and functional organization of biological systems. Topics include the roles of free energy, diffusion, electromotive forces, non-equilibrium dynamics, and information in fundamental biological processes.
Terms: Win
| Units: 3-4
BIO 128:
Geographic Impacts of Climate Change: Mapping the Stories
Climate change imparts political, socioeconomic and ecological impacts worldwide, creating an urgent need for scientists to communicate with policy-makers. Students will collect data for a region of the US from multiple sources ranging from academic journals to popular media to create an interactive Story Map (http://storymaps.arcgis.com) that merges the scientific and human dimensions of climate change. Students will present this map to state and national policy-makers. Students enrolled in 3 credits will have an emphasis on engagement of community partners in addition to normal class participation.
Terms: Spr
| Units: 2-3
BIO 129A:
Cellular Dynamics I: Cell Motility and Adhesion
Cell motility emphasizing role of actin assembly and dynamics coupling actin organization to cell movement. Interaction of cells with extracellular matrix, and remodelling of extracellular matrix in development and disease. Directed cell migration by chemotaxis (neuronal path-finding, immune cells). Cell-cell adhesion, formation of intercellular junctions and mechanisms regulating cell-cell interactions in development and diseases. Emphasis is on experimental logic, methods, problem solving, and interpretation of results. Students present research papers. Satisfies Central Menu Area 2. Prerequisite: Biology core.
Terms: Win
| Units: 4
| UG Reqs: GER: DB-NatSci, WAY-AQR, WAY-SMA
BIO 129B:
Cellular Dynamics II: Building a Cell
Principles of cell organization; how common biochemical pathways are modified to generate diversity in cell structure and function. Roles of actin and microtubule cytoskeletons in cellular architecture. Mechanisms of protein sorting and trafficking, and protein modules and switches in regulating cell polarity. Yeast to polarized epithelial cells and neurons. Emphasis is on experimental logic, methods, problem solving, and interpretation of results. Students present research papers. Satisfies Central Menu Area 2. Prerequisite: Biology core. Recommended: 129A.
Terms: Spr
| Units: 4
| UG Reqs: GER: DB-NatSci
BIO 131:
Complex Systems Lab
The behavior of complex systems will be explored in this seminar through hands-on experiments and computer simulations. Nonlinearity, fractals, chaos, and self-organization concepts will be studied through double pendulums, BZ reactions, chaotic video feedback, and social experiments. Emphasis will be placed on the experiments while readings, programming using NetLogo, and mathematical derivations will be used to supplement learning. Graduate student led seminar.
Terms: Aut
| Units: 1
| Repeatable
for credit
BIO 132:
Advanced Imaging Lab in Biophysics (APPPHYS 232, BIO 232, BIOPHYS 232, GENE 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
| UG Reqs: GER: DB-NatSci
BIO 136:
Evolutionary Paleobiology
A paleontological approach to evolutionary theory. Topics: history of life, speciation, heterochrony, evolutionary constraint, coevolution, macroevolution, the Cambrian Explosion, mass extinctions, taphonomy, life on land, life in the sea, life in the air. Satisfies Central Menu Area 4. Prerequisite: Biology Core.
Last offered: Winter 2011
| Units: 4
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 137:
Plant Genetics (BIO 237)
Gene analysis, mutagenesis, transposable elements; developmental genetics of flowering and embryo development; biochemical genetics of plant metabolism; scientific and societal lessons from transgenic plants. Satisfies Central Menu Area 2. Prerequisite: Biology core or consent of instructor. Satisfies WIM in Biology.
Terms: Spr
| Units: 3-4
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 139:
Biology of Birds
How birds interact with their environments and each other, emphasizing studies that had impact in the fields of population biology, community ecology, and evolution. Local bird communities. Emphasis is on field research. Enrollment limited to 20. Prerequisites: 43 or equivalent, and consent of instructor. Recommended: birding experience.
Last offered: Spring 2013
| Units: 3
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 13N:
Environmental Problems and Solutions
Preference to freshmen. Students do independent investigations of current environmental problems, analyzing differing views of them and discussing possible solutions. Each student gives seminar presentations and leads seminar discussions. Short, documented position papers are written for policy makers.
| Units: 3
| UG Reqs: GER: DB-NatSci
BIO 141:
Biostatistics (STATS 141)
Introductory statistical methods for biological data: describing data (numerical and graphical summaries); introduction to probability; and statistical inference (hypothesis tests and confidence intervals). Intermediate statistical methods: comparing groups (analysis of variance); analyzing associations (linear and logistic regression); and methods for categorical data (contingency tables and odds ratio). Course content integrated with statistical computing in R.
Terms: Aut
| Units: 3-5
| UG Reqs: GER:DB-Math, WAY-AQR
BIO 144:
Conservation Biology: A Latin American Perspective (BIO 234, HUMBIO 112)
Principles and application of the science of preserving biological diversity. Conceptually, this course is designed to explore 4 major components relevant to the conservation of biodiversity, as exemplified by the Latin American region. The conceptual frameworks and principles, however, should be generally applicable, and provide insights for all regions of the world, including those of lesser biodiversity. Satisfies Central Menu Area 4 for Bio majors. Prerequisite: BIO 101, or BIO 43 or HUMBIO 2A with consent of instructor. Graduate level students will be expected to conduct a literature research exercise leading to a written paper, addressing a topic of their choosing, derived from any of the themes discussed in class.
Terms: Spr
| Units: 3
| UG Reqs: GER: DB-NatSci
BIO 146:
Population Studies
Series of talks by distinguished speakers introducing approaches to population and resource studies.
Terms: Win
| Units: 1
| Repeatable
for credit
BIO 149:
The Neurobiology of Sleep (BIO 249, HUMBIO 161)
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.
Last offered: Winter 2013
| Units: 4
| UG Reqs: GER: DB-NatSci
BIO 150:
Human Behavioral Biology (BIO 250, 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
| Units: 5
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 151:
Mechanisms of Neuron Death
For Biology majors with background in neuroscience. Cell and molecular biology of neuron death during neurological disease. Topics: the amyloid diseases (Alzheimer's), prion diseases (kuru and Creutzfeldt-Jakob), oxygen radical diseases (Parkinson's and ALS), triplet repeat diseases (Huntington's), and AIDS-related dementia. Student presentations. Enrollment limited to 15; application required.
Terms: Aut
| Units: 3
| UG Reqs: GER: DB-NatSci
BIO 153:
Cellular Neuroscience: Cell Signaling and Behavior (PSYCH 120)
Neural interactions underlying behavior. Prerequisites: PSYCH 1 or basic biology.
Terms: Aut
| Units: 4
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 154:
Molecular and Cellular Neurobiology
For advanced undergraduate 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. Satisfies Central Menu Areas 2 or 3 for Bio majors. Prerequisite for undergraduates: Biology core or equivalent, or consent of instructors.
| Units: 4
| UG Reqs: GER: DB-NatSci
BIO 156:
Epigenetics (BIO 256)
Epigenetics is the process by which phenotypes not determined by the DNA sequence are stably inherited in successive cell divisions. Course will cover the molecular mechanisms governing epigenetics, ranging from the discovery of epigenetic phenomena to present-day studies on the role of chromatin, DNA methylation, and RNA in regulating epigenetics processes. Topics include: position effect gene expression, genome regulation, gene silencing & heterochromatin, histone code, DNA methylation & imprinting, epigenetics & disease, and epigenetic-based therapeutics. Prerequisite: BIO41 and BIO42 or consent of instructor.
Terms: Spr
| Units: 2
BIO 157:
Biochemistry and Molecular Biology of Plants (BIO 257)
Biochemical and molecular basis of plant growth and adaptation. Topics include: hormone signal transduction; photoreceptor chemistry and signaling; metabolite sensing and transport; dynamics of photosynthesis; plant innate immunity and symbiosis. Lectures and readings will emphasize research methods. Prerequisite: Biology core or equivalent, or consent of instructor.
Terms: Spr
| Units: 3-4
| UG Reqs: GER: DB-NatSci
BIO 158:
Developmental Neurobiology (BIO 258)
For advanced undergraduates and coterminal students. The principles of nervous system development from the molecular control of patterning, cell-cell interactions, and trophic factors to the level of neural systems and the role of experience in influencing brain structure and function. 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. Satisfies Central Menu Areas 2 or 3. Prerequisite: BIO 42 or equivalent.
Last offered: Spring 2013
| Units: 4
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 160A:
Developmental Biology I
Focus is on the molecular mechanisms underlying the generation of diverse cell types and tissues during embryonic and post-embryonic animal development. The role of cell-cell communication in controlling key developmental decisions. Topics covered in this quarter include embryonic axis formation, morphogen signaling, cell type specification and stem cells. Experimental logic and methods of research in developmental biology. Discussions of research papers. Satisfies Central Menu Areas 1 or 2. Prerequisite: Biology core or consent of instructor.
Terms: Aut
| Units: 4
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 160B:
Developmental Biology II
Continuation of BIO 160A. Focus is on the molecular mechanisms underlying the generation of diverse cell types and tissues during embryonic and post-embryonic animal development. The role of cell-cell communication in controlling key developmental decisions. The topics include sexual control of development, tissue polarity and growth, cell migration, regeneration, and the evolution of developmental mechanisms. Experimental logic and methods of research in developmental biology. Discussions of research papers. Satisfies Central Menu Areas 1 or 2. Prerequisites: Biology Core and 160A, or consent of instructor.
Terms: Win
| Units: 4
| UG Reqs: GER: DB-NatSci
BIO 161:
Molecular Basis of Biological Communication
Across molecular, cellular, organismal and communal biological scales, communication among elements of a system is required for its function. The molecules and logic at the heart of communication at levels from the interactions between cells in a developing body to how organisms perceive and respond to their physical environment and the organisms around them; how these systems normally work and how failures in communication result in and from disease. Current research literature. Prerequisites: BIO 41, 42. Recommended: BIO 160A, 129A.
Last offered: Spring 2011
| Units: 4
| UG Reqs: WAY-SMA
BIO 162:
Lessons in Ecological Restoration: Israel and the Middle East (JEWISHST 116)
The environment in the Middle East reflects the impacts of millennia of continued human activities, with degraded soils, biodiversity loss and contaminated water resources. In a trial and error process since its inception, Israel has pursued an ambitious program of ecological restoration through afforestation, aggressive water management and environmental conservation. This course evaluates the effectiveness of different environmental policies from ecological perspectives. It also assesses potential regional ecological cooperation as part of a Middle Eastern peace process.
Terms: Aut
| Units: 3
BIO 165:
Molecular and Cellular Mechanisms of Neurological Disease
Current topics in research and investigative therapies of neurological disorders, including epilepsy, OCD, Alzheimer's disease, stroke and multiple sclerosis. Analysis and discussion of primary research papers as well as sources directed at general public. Emphasis on critical thinking, experimental design, therapeutic approaches. Guest lecturers include Dr. Lawrence Steinman and Dr. Gary Steinberg."
Terms: Win
| Units: 1
BIO 168:
Explorations in Stem Cell Biology
A discussion-based course for advanced undergraduates. The purpose of this course is to introduce students to key topics in stem cell biology. Review and discussion of some landmark and current primary literature in the stem cell field. Topics will include embryonic and adult stem cells, cellular reprogramming and stem cells in disease and regenerative medicine. Students will analyze and discuss primary literature and present a current research paper in their preferred stem cell topic area. Prerequisites: Biology or Human Biology core.
Terms: Aut
| Units: 1
BIO 174:
Human Skeletal Anatomy (ANTHRO 175, ANTHRO 275, BIO 274, HUMBIO 180)
Study of the human skeleton (a. k. a. human osteology), as it bears on other disciplines, including medicine, forensics, archaeology, and paleoanthropology (human evolution). Basic bone biology, anatomy, and development, emphasizing hands-on examination and identification of human skeletal parts, their implications for determining an individual¿s age, sex, geographic origin, and health status, and for the evolutionary history of our species. Three hours of lecture and at least three hours of supervised and independent study in the lab each week.
Terms: Win
| Units: 5
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 177:
Plant Microbe Interaction (BIO 277)
Molecular basis of plant symbiosis and pathogenesis. Topics include mechanisms of recognition and signaling between microbes and plant hosts, with examples such as the role of small molecules, secreted peptides, and signal transduction pathways in symbiotic or pathogenic interactions. Readings include landmark papers together with readings in the contemporary literature. Prerequisites: Biology core and two or more upper division courses in genetics, molecular biology, or biochemistry. Recommended: plant genetics or plant biochemistry.
Terms: Spr
| Units: 3
BIO 178:
Microbiology Literature (BIO 278)
For advanced undergraduates and first-year graduate students. Critical reading of the research literature in prokaryotic genetics and molecular biology, with particular applications to the study of major human pathogens. Classic and foundational papers in pathogenesis, genetics, and molecular biology; recent literature on bacterial pathogens such as Salmonella, Vibrio, and/or Yersinia. Diverse experimental approaches: biochemistry, genomics, pathogenesis, and cell biology. Prerequisites: Biology Core and two upper-division courses in genetics, molecular biology, or biochemistry.
Terms: Win
| Units: 3
BIO 181:
Human Genetic Variation
The geographic distribution of human genetic variation; the genetic perspective on ancient and recent human migrations; quantitative methods for inference of human evolutionary history from patterns of genetic variation. Connections of human genetic variation to current topics such as ancestry testing, DNA forensics, and identification of disease genes. Prerequisites; Bio or HumBio core, calculus.
Terms: Win
| Units: 3
BIO 182:
Modeling Cultural Evolution (BIO 282)
Seminar. Quantitative models for the evolution of socially transmitted traits. Rates of change of learned traits in populations and patterns of cultural diversity as a function of innovation and cultural transmission. Learning in constant and changing environments. Possible avenues for gene-culture coevolution.
Terms: Spr
| Units: 3
BIO 183:
Theoretical Population Genetics (BIO 283)
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
BIO 188:
Biochemistry I (BIO 288, 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. Satisfies Central Menu Area 1 for Bio majors. Prerequisites: CHEM 33, 35, 131, and 135 or 171.
Terms: Aut
| Units: 3
| UG Reqs: GER: DB-NatSci
BIO 189:
Biochemistry II (BIO 289, 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. Satisfies Central Menu Area 1 for Bio majors. Prerequisite: BIO 188/288 or CHEM 181 or CHEMENG 181/281 (formerly 188/288).
Terms: Win
| Units: 3
| UG Reqs: GER: DB-NatSci
BIO 18Q:
Plant Evolutionary Ecology
Plant EcoEvo analyzes the conceptual basis of ecology and evolution from the plants' perspective. After a broad overview of the biomes of the world, it explores population ecology, community ecology and biotic interactions. This is followed by an analysis of biodiversity from the botanical perspective and closes with a discussion of anthropogenic impact on plants. The course is based on lectures and practical activities (discussion of selected papers; analysis of data; laboratory activities, 2 field trips). Emphasis: Latin American ecosystems.
| Units: 3
BIO 196A:
Biology Senior Reflection
Capstone course series for seniors. Creative, self-reflective and scientifically relevant projects conceived, produced and exhibited over the course of three quarters. Explore scientific content of personal interest through creative forms including but not limited to writing, music, fine arts, performing arts, photography, film or new media. A written essay on the creative process and scientific significance of the selected topic will accompany the creative work. Completed projects may be included in a creative portfolio. Required enrollment in 196A,B,C. Satisfies WIM in Biology.
Terms: Aut
| Units: 3
BIO 196B:
Biology Senior Reflection
Capstone course series for seniors. Creative, self-reflective and scientifically relevant projects conceived, produced and exhibited over the course of three quarters. Explore scientific content of personal interest through creative forms including but not limited to writing, music, fine arts, performing arts, photography, film or new media. A written essay on the creative process and scientific significance of the selected topic will accompany the creative work. Completed projects may be included in a creative portfolio. Required enrollment in 196A,B,C.
Terms: Win
| Units: 3
| UG Reqs: WAY-CE
BIO 196C:
Biology Senior Reflection
Capstone course series for seniors. Creative, self-reflective and scientifically relevant projects conceived, produced and exhibited over the course of three quarters. Explore scientific content of personal interest through creative forms including but not limited to writing, music, fine arts, performing arts, photography, film or new media. A written essay on the creative process and scientific significance of the selected topic will accompany the creative work. Completed projects may be included in a creative portfolio. Required enrollment in 196A,B,C.
Terms: Spr
| Units: 3
| UG Reqs: WAY-CE
BIO 197WA:
Senior Writing Project: The Personal Essay in Biology
Seminar focused on writing. Compose, workshop and revise scientifically relevant and personal essays in biology directed at a mainstream audience, interweaving research, interview, memoir, and other elements of nonfiction craft. Satisfies WIM in Biology.
Terms: Win
| Units: 3
BIO 198:
Directed Reading in Biology
Individually arranged under the supervision of members of the faculty.
Terms: Aut, Win, Spr, Sum
| Units: 1-15
| Repeatable
10 times
(up to 60 units total)
Instructors: ;
Barton, K. (PI);
Bergmann, D. (PI);
Berry, J. (PI);
Block, B. (PI);
Block, S. (PI);
Boggs, C. (PI);
Crowder, L. (PI);
Cyert, M. (PI);
Daily, G. (PI);
Denny, M. (PI);
Dirzo, R. (PI);
Ehrlich, P. (PI);
Epel, D. (PI);
Feldman, M. (PI);
Fernald, R. (PI);
Field, C. (PI);
Fraser, H. (PI);
Frommer, W. (PI);
Frydman, J. (PI);
Fukami, T. (PI);
Gilly, W. (PI);
Gordon, D. (PI);
Gozani, O. (PI);
Grossman, A. (PI);
Hadly, E. (PI);
Hanawalt, P. (PI);
Heller, H. (PI);
Jones, P. (PI);
Khalfan, W. (PI);
Klein, R. (PI);
Kopito, R. (PI);
Long, S. (PI);
Lowe, C. (PI);
Luo, L. (PI);
McConnell, S. (PI);
Micheli, F. (PI);
Mooney, H. (PI);
Morrison, A. (PI);
Mudgett, M. (PI);
Nelson, W. (PI);
Palumbi, S. (PI);
Petrov, D. (PI);
Red-Horse, K. (PI);
Rosenberg, N. (PI);
Roughgarden, J. (PI);
Sapolsky, R. (PI);
Schnitzer, M. (PI);
Shatz, C. (PI);
Shen, K. (PI);
Simon, M. (PI);
Simoni, R. (PI);
Skotheim, J. (PI);
Somero, G. (PI);
Stearns, T. (PI);
Thompson, S. (PI);
Todhunter, A. (PI);
Tuljapurkar, S. (PI);
Vitousek, P. (PI);
Walbot, V. (PI);
Wang, Z. (PI);
Watt, W. (PI);
Collins, J. (GP)
BIO 198X:
Out-of-Department Directed Reading
Individually arranged under the supervision of members of the faculty. Credit for work arranged with out-of-department faculty is restricted to Biology majors and requires department approval. See http://biohonors.stanford.edu for information and petitions. May be repeated for credit.
Terms: Aut, Win, Spr, Sum
| Units: 1-15
| Repeatable
10 times
(up to 60 units total)
Instructors: ;
Bergmann, D. (PI);
Block, B. (PI);
Block, S. (PI);
Boggs, C. (PI);
Chan, P. (PI);
Chu, L. (PI);
Cimprich, K. (PI);
Clandinin, T. (PI);
Contag, C. (PI);
Cooke, J. (PI);
Crowder, L. (PI);
Cyert, M. (PI);
Daily, G. (PI);
Darian-Smith, C. (PI);
Denny, M. (PI);
Dirzo, R. (PI);
Ehrlich, P. (PI);
Feldman, M. (PI);
Fernald, R. (PI);
Field, C. (PI);
Fraser, H. (PI);
Frommer, W. (PI);
Frydman, J. (PI);
Fukami, T. (PI);
Gardner, C. (PI);
Gilly, W. (PI);
Gold, G. (PI);
Goodman, M. (PI);
Goodman, S. (PI);
Gordon, D. (PI);
Gozani, O. (PI);
Hadly, E. (PI);
Hallmayer, J. (PI);
Hanawalt, P. (PI);
Heilshorn, S. (PI);
Heller, H. (PI);
Herzenberg, L. (PI);
Hestrin, S. (PI);
Hsu, S. (PI);
Jones, P. (PI);
Khalfan, W. (PI);
Khavari, P. (PI);
Klein, R. (PI);
Kobilka, B. (PI);
Koong, A. (PI);
Kopito, R. (PI);
Krams, S. (PI);
Kuo, C. (PI);
Levy, R. (PI);
Lipsick, J. (PI);
Long, S. (PI);
Lowe, C. (PI);
Luo, L. (PI);
Lyons, D. (PI);
Maduke, M. (PI);
Manber, R. (PI);
McConnell, S. (PI);
Micheli, F. (PI);
Michie, S. (PI);
Mooney, H. (PI);
Morrison, A. (PI);
Mudgett, M. (PI);
Nelson, W. (PI);
Ormond, K. (PI);
Palumbi, S. (PI);
Peehl, D. (PI);
Petrov, D. (PI);
Raymond, J. (PI);
Red-Horse, K. (PI);
Root, T. (PI);
Rosenberg, N. (PI);
Sapolsky, R. (PI);
Sarnow, P. (PI);
Schnitzer, M. (PI);
Shatz, C. (PI);
Shen, K. (PI);
Simon, M. (PI);
Simoni, R. (PI);
Skotheim, J. (PI);
Somero, G. (PI);
Spormann, A. (PI);
Stearns, T. (PI);
Steinberg, G. (PI);
Thompson, S. (PI);
Tuljapurkar, S. (PI);
Vitousek, P. (PI);
Walbot, V. (PI);
Watt, W. (PI);
Weissman, I. (PI);
Wine, J. (PI);
Yang, Y. (PI);
Collins, J. (GP)
BIO 199:
Advanced Research Laboratory in Experimental Biology
Individual research taken by arrangement with in-department instructors. See http://biohonors.stanford.edu for information on research sponsors, units, and credit for summer research. May be repeated for credit.
Terms: Aut, Win, Spr, Sum
| Units: 1-15
| Repeatable
15 times
(up to 60 units total)
Instructors: ;
Barton, K. (PI);
Bergmann, D. (PI);
Berry, J. (PI);
Block, B. (PI);
Block, S. (PI);
Boggs, C. (PI);
Crowder, L. (PI);
Cyert, M. (PI);
Daily, G. (PI);
Denny, M. (PI);
Dirzo, R. (PI);
Dixon, S. (PI);
Ehrlich, P. (PI);
Epel, D. (PI);
Feldman, J. (PI);
Feldman, M. (PI);
Fernald, R. (PI);
Field, C. (PI);
Fraser, H. (PI);
Frommer, W. (PI);
Frydman, J. (PI);
Fukami, T. (PI);
Gilly, W. (PI);
Gordon, D. (PI);
Gozani, O. (PI);
Grossman, A. (PI);
Hadly, E. (PI);
Hanawalt, P. (PI);
Heller, H. (PI);
Jones, P. (PI);
Jonikas, M. (PI);
Klein, R. (PI);
Kopito, R. (PI);
Long, S. (PI);
Lowe, C. (PI);
Luo, L. (PI);
McConnell, S. (PI);
Micheli, F. (PI);
Mooney, H. (PI);
Morrison, A. (PI);
Mudgett, M. (PI);
Nelson, W. (PI);
Palumbi, S. (PI);
Peay, K. (PI);
Petrov, D. (PI);
Red-Horse, K. (PI);
Rosenberg, N. (PI);
Roughgarden, J. (PI);
Sapolsky, R. (PI);
Schnitzer, M. (PI);
Shatz, C. (PI);
Shen, K. (PI);
Simon, M. (PI);
Simoni, R. (PI);
Skotheim, J. (PI);
Somero, G. (PI);
Stearns, T. (PI);
Thompson, S. (PI);
Tuljapurkar, S. (PI);
Vitousek, P. (PI);
Walbot, V. (PI);
Wang, Z. (PI);
Watt, W. (PI);
Collins, J. (GP)
BIO 199W:
Senior Honors Thesis: How to Effectively Write About Scientific Research
Workshop. For seniors pursuing an honors thesis in a biology-focused major or program. Focus on improving scientific writing and synthesizing in the context of students' individual research projects. Complete literature review which will form the basis for the thesis introduction. Develop methods section of the thesis. Small seminar-style discussion sections with research-based discussions, student led PowerPoint presentations, and writing workshops. Co-requisite: Concurrent enrollment in 199 or 199X or equivalent. Satisfies WIM in Biology.
Terms: Win
| Units: 3
BIO 199X:
Out-of-Department Advanced Research Laboratory in Experimental Biology
Individual research by arrangement with out-of-department instructors. Credit for 199X is restricted to declared Biology majors and requires department approval. See http://biohonors.stanford.edu for information on research sponsors, units, petitions, deadlines, credit for summer research, and out-of-Stanford research. May be repeated for credit.
Terms: Aut, Win, Spr, Sum
| Units: 1-15
| Repeatable
15 times
(up to 60 units total)
Instructors: ;
Adler, J. (PI);
Agras, W. (PI);
Altman, R. (PI);
Andriacchi, T. (PI);
Ariagno, R. (PI);
Arrigo, K. (PI);
Artandi, S. (PI);
Arvin, A. (PI);
Attardi, L. (PI);
Axelrod, J. (PI);
Baker, J. (PI);
Barr, D. (PI);
Barres, B. (PI);
Barsh, G. (PI);
Barton, K. (PI);
Bass, D. (PI);
Batzoglou, S. (PI);
Beachy, P. (PI);
Bergmann, D. (PI);
Bernstein, D. (PI);
Bhalla, V. (PI);
Blaschke, T. (PI);
Blau, H. (PI);
Block, B. (PI);
Block, S. (PI);
Boehm, A. (PI);
Boggs, C. (PI);
Bogyo, M. (PI);
Boothroyd, J. (PI);
Bouley, D. (PI);
Boxer, L. (PI);
Boxer, S. (PI);
Briggs, W. (PI);
Brown, J. (PI);
Brown, P. (PI);
Brundage, S. (PI);
Brunet, A. (PI);
Brunger, A. (PI);
Brutlag, D. (PI);
Buckmaster, P. (PI);
Buckwalter, M. (PI);
Butcher, E. (PI);
Calos, M. (PI);
Cartwright, C. (PI);
Cavalli-Sforza, L. (PI);
Chan, P. (PI);
Chang, H. (PI);
Chang, K. (PI);
Chang, S. (PI);
Chase, R. (PI);
Chawla, A. (PI);
Chen, J. (PI);
Cheng, A. (PI);
Chien, Y. (PI);
Chu, G. (PI);
Cimprich, K. (PI);
Clandinin, T. (PI);
Clarke, M. (PI);
Clayberger, C. (PI);
Cleary, M. (PI);
Cochran, J. (PI);
Cohen, H. (PI);
Cohen, S. (PI);
Collman, J. (PI);
Conley, F. (PI);
Constantinou, C. (PI);
Contag, C. (PI);
Cooke, J. (PI);
Cooper, A. (PI);
Crabtree, G. (PI);
Criddle, C. (PI);
Crowder, L. (PI);
Cyert, M. (PI);
Daily, G. (PI);
Dalman, R. (PI);
Darian-Smith, C. (PI);
Das, R. (PI);
Davis, M. (PI);
Davis, R. (PI);
Deisseroth, K. (PI);
Dement, W. (PI);
Denny, M. (PI);
Dhabhar, F. (PI);
Dirzo, R. (PI);
Dolmetsch, R. (PI);
Doniach, S. (PI);
Dorfman, L. (PI);
Dragoo, J. (PI);
Ehrhardt, D. (PI);
Ehrlich, P. (PI);
Eng, L. (PI);
Engleman, E. (PI);
Epel, D. (PI);
Falcon, W. (PI);
Falkow, S. (PI);
Fathman, C. (PI);
Feldman, B. (PI);
Feldman, D. (PI);
Feldman, M. (PI);
Felsher, D. (PI);
Fernald, R. (PI);
Ferrell, J. (PI);
Field, C. (PI);
Fire, A. (PI);
Ford, J. (PI);
Fortmann, S. (PI);
Foung, S. (PI);
Francke, U. (PI);
Fraser, H. (PI);
Fredericson, M. (PI);
Friedlander, A. (PI);
Froelicher, V. (PI);
Frommer, W. (PI);
Frydman, J. (PI);
Fukami, T. (PI);
Fuller, M. (PI);
Furthmayr, H. (PI);
Galli, S. (PI);
Gambhir, S. (PI);
Garcia, G. (PI);
Gardner, P. (PI);
Garner, C. (PI);
Garner, J. (PI);
Gesundheit, N. (PI);
Giaccia, A. (PI);
Gilly, W. (PI);
Girod, S. (PI);
Giudice, L. (PI);
Glenn, J. (PI);
Gold, G. (PI);
Goodman, M. (PI);
Goodman, S. (PI);
Gordon, D. (PI);
Gozani, O. (PI);
Gray, G. (PI);
Greenberg, H. (PI);
Greicius, M. (PI);
Guilleminault, C. (PI);
Guzman, R. (PI);
Hadly, E. (PI);
Hallmayer, J. (PI);
Hanawalt, P. (PI);
Haskell, W. (PI);
Heilshorn, S. (PI);
Heller, H. (PI);
Heller, S. (PI);
Helms, J. (PI);
Herschlag, D. (PI);
Herzenberg, L. (PI);
Hestrin, S. (PI);
Hodgson, K. (PI);
Hoffman, A. (PI);
Hoffman, B. (PI);
Hogness, D. (PI);
Hsieh, M. (PI);
Hsu, S. (PI);
Hsueh, A. (PI);
Huestis, W. (PI);
Huguenard, J. (PI);
Jackson, P. (PI);
Jardetzky, O. (PI);
Jones, P. (PI);
Jonikas, M. (PI);
Kahn, D. (PI);
Kaiser, A. (PI);
Karasek, M. (PI);
Katzenstein, D. (PI);
Kay, M. (PI);
Kendig, J. (PI);
Khavari, P. (PI);
Kim, S. (PI);
King, A. (PI);
Kingsley, D. (PI);
Kirkegaard, K. (PI);
Klein, R. (PI);
Knope, M. (PI);
Knox, S. (PI);
Knudsen, E. (PI);
Knutson, B. (PI);
Kobilka, B. (PI);
Koong, A. (PI);
Kopito, R. (PI);
Kornberg, A. (PI);
Kornberg, R. (PI);
Koseff, J. (PI);
Kraemer, F. (PI);
Krams, S. (PI);
Krasnow, M. (PI);
Krensky, A. (PI);
Kuo, C. (PI);
Lee, P. (PI);
Lehman, I. (PI);
Leung, L. (PI);
Levenston, M. (PI);
Levy, R. (PI);
Levy, S. (PI);
Lewis, D. (PI);
Lewis, R. (PI);
Li, G. (PI);
Lipsick, J. (PI);
Litt, I. (PI);
Long, S. (PI);
Longaker, M. (PI);
Lorenz, H. (PI);
Lowe, A. (PI);
Lowe, C. (PI);
Lu, B. (PI);
Luo, L. (PI);
Lyons, D. (PI);
MacIver, M. (PI);
Mackey, S. (PI);
Madison, D. (PI);
Maduke, M. (PI);
Majeti, R. (PI);
Maldonado, Y. (PI);
Malenka, R. (PI);
Marcus, R. (PI);
Marinkovich, M. (PI);
Marmor, M. (PI);
Martinez, O. (PI);
Matheson, G. (PI);
Matin, A. (PI);
McConnell, H. (PI);
McConnell, S. (PI);
McDevitt, H. (PI);
McKay, D. (PI);
McMahan, U. (PI);
Mellins, E. (PI);
Menon, V. (PI);
Merigan, T. (PI);
Micheli, F. (PI);
Michie, S. (PI);
Mignot, E. (PI);
Miklos, D. (PI);
Miller, D. (PI);
Mobley, W. (PI);
Mocarski, E. (PI);
Mochly-Rosen, D. (PI);
Monack, D. (PI);
Monje-Deisseroth, M. (PI);
Mooney, H. (PI);
Morris, R. (PI);
Morrison, A. (PI);
Morton, J. (PI);
Mudgett, M. (PI);
Murphy, G. (PI);
Myers, B. (PI);
Myers, R. (PI);
Nadeau, K. (PI);
Neely, E. (PI);
Negrin, R. (PI);
Nelson, W. (PI);
Newsome, W. (PI);
Nicolls, M. (PI);
Nishino, S. (PI);
Nolan, G. (PI);
Nusse, R. (PI);
Oro, A. (PI);
Palmer, T. (PI);
Palumbi, S. (PI);
Pande, V. (PI);
Parham, P. (PI);
Parker, K. (PI);
Parnes, J. (PI);
Parsonnet, J. (PI);
Patterson, D. (PI);
Payne, J. (PI);
Pearl, R. (PI);
Pecora, R. (PI);
Peebles, R. (PI);
Peehl, D. (PI);
Petrov, D. (PI);
Pfeffer, S. (PI);
Pollack, J. (PI);
Porteus, M. (PI);
Porzig, E. (PI);
Prince, D. (PI);
Pringle, J. (PI);
Puglisi, J. (PI);
Quertermous, T. (PI);
Rabinovitch, M. (PI);
Raffin, T. (PI);
Rando, T. (PI);
Rasgon, N. (PI);
Raymond, J. (PI);
Reaven, G. (PI);
Red-Horse, K. (PI);
Reijo Pera, R. (PI);
Reimer, R. (PI);
Reiss, A. (PI);
Relman, D. (PI);
Riedel-Kruse, I. (PI);
Robbins, R. (PI);
Robertson, C. (PI);
Robinson, B. (PI);
Robinson, T. (PI);
Rockson, S. (PI);
Rohatgi, R. (PI);
Root, T. (PI);
Rosen, G. (PI);
Rosenberg, N. (PI);
Roth, R. (PI);
Rothschild, L. (PI);
Roughgarden, J. (PI);
Ruiz-Lozano, P. (PI);
Sage, J. (PI);
Sakamoto, K. (PI);
Sapolsky, R. (PI);
Sarnow, P. (PI);
Schatzberg, A. (PI);
Schneider, D. (PI);
Schnitzer, M. (PI);
Schoolnik, G. (PI);
Schrier, S. (PI);
Schwarz, T. (PI);
Scott, M. (PI);
Shapiro, L. (PI);
Shatz, C. (PI);
Shen, K. (PI);
Sherlock, G. (PI);
Shochat, S. (PI);
Shooter, E. (PI);
Shrager, J. (PI);
Sibley, E. (PI);
Sikic, B. (PI);
Silverberg, G. (PI);
Simon, M. (PI);
Simoni, R. (PI);
Singh, U. (PI);
Skirboll, S. (PI);
Skotheim, J. (PI);
Smith, M. (PI);
Smith, R. (PI);
Smith, S. (PI);
Smolke, C. (PI);
Snyder, M. (PI);
Somero, G. (PI);
Spiegel, D. (PI);
Spormann, A. (PI);
Spudich, J. (PI);
Stamey, T. (PI);
Stearns, T. (PI);
Steele, C. (PI);
Steinberg, G. (PI);
Steinman, L. (PI);
Stevens, D. (PI);
Stevenson, D. (PI);
Stockdale, F. (PI);
Straight, A. (PI);
Strober, S. (PI);
Stryer, L. (PI);
Sudhof, T. (PI);
Sullivan, E. (PI);
Sun, Z. (PI);
Sweet-Cordero (PI);
Ta, C. (PI);
Talbot, W. (PI);
Tan, M. (PI);
Taylor, C. (PI);
Teng, N. (PI);
Theriot, J. (PI);
Thompson, S. (PI);
Todhunter, A. (PI);
Triadafilopoulos, G. (PI);
Tsao, P. (PI);
Tse, V. (PI);
Tsien, R. (PI);
Tuljapurkar, S. (PI);
Utz, P. (PI);
Vemuri, M. (PI);
Villeneuve, A. (PI);
Vitousek, P. (PI);
Vollrath, D. (PI);
Walbot, V. (PI);
Wandless, T. (PI);
Wang, T. (PI);
Wang, X. (PI);
Watt, W. (PI);
Waymouth, R. (PI);
Weinberg, K. (PI);
Weis, W. (PI);
Weissman, I. (PI);
Wernig, M. (PI);
Whitlock, J. (PI);
Wine, J. (PI);
Winograd, C. (PI);
Wong, A. (PI);
Wong, D. (PI);
Wu, J. (PI);
Wu, S. (PI);
Wyss-Coray, T. (PI);
Yang, F. (PI);
Yang, P. (PI);
Yang, Y. (PI);
Yao, M. (PI);
Zajac, F. (PI);
Zare, R. (PI);
Zarins, C. (PI);
Zehnder, J. (PI);
Zeitzer, J. (PI);
Zhao, H. (PI);
de Lecea, L. (PI);
Collins, J. (GP);
Frank, D. (GP);
Jones, D. (GP);
Kuhn, R. (GP);
Riley, R. (GP)
BIO 20:
Introduction to Brain and Behavior (HUMBIO 21)
Evolutionary principles to understand how the brain regulates behavior physiologically, and is also influenced by behavioral interactions. Topics include neuron structure and function, transmission of neural information, anatomy and physiology of sensory and motor systems, regulation of body states, the biological basis of learning and memory, and behavioral abnormalities.
| Units: 3
| UG Reqs: GER: DB-NatSci
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. Satisfies Central Menu Area 1. Prerequisite: Biology core.
Terms: Win
| Units: 5
BIO 202:
Ecological Statistics
Intended for graduate students (and advanced undergraduates in special circumstances with consent of instructors) in biology and related environmental sciences, this course is an introduction to statistical methods for ecological data analysis, using the programming language R. The course will have lectures, discussions, and independent research projects using the students' own data or simulated or publicly available data.
Terms: Win
| Units: 3
BIO 209A:
The Human Genome and Disease (BIO 109A, BIOC 109A, BIOC 209A, 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. Students with a major, minor or coterm in Biology: 109A/209A or 109B/209B may count toward degree program but not both.
Terms: Win
| Units: 3
BIO 209B:
The Human Genome and Disease: Genetic Diversity and Personalized Medicine (BIO 109B, BIOC 109B, BIOC 209B)
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. Students with a major, minor or coterm in Biology: 109A/209A or 109B/209B may count toward degree program but not both.
Terms: Spr
| Units: 3
BIO 20N:
Learning Creativity in Biology through Finding a Good Problem and Searching for Innovative Solutions
This course will explore how we can learn to be creative in biology. Examples of interesting problems include energy limitation, food security, species conservation and climate change. Once we agree on a problem to tackle, students will work in groups to find similar problems and solutions in other fields, construct a new solution together and debate positive and negative aspects of the solution to refine it. Students will gain experience in reading primary literature, innovative thinking, speaking and listening skills.
| Units: 3
BIO 210:
DNA Replication and Genomic Maintenance (BIO 110)
Maintenance of the genome and its accurate replication are prerequisites for life. DNA replication is also intricately connected to pathways for responding to genotoxic stress, which include inevitable collisions with transcription. In eukaryotes, DNA repair and replication are tightly connected to chromatin modification. Emphasis for lecture topics include: DNA-templated chromatin transactions; Chromatin manipulation during replication and DNA damage responses; Structural biology and molecular mechanisms of replication and DNA repair enzymes; Inducible responses to genotoxic stress; Relationships of DNA damage processing to mutagenesis, carcinogenesis, aging and human genetic disease.
Terms: Spr
| Units: 3
BIO 212:
Human Physiology (BIO 112, HUMBIO 133)
Human physiology will be examined by organ systems: respiratory, cardiovascular, renal, and gastrointestinal. Concepts of cell and molecular biology that underlie organ development, pathophysiology and opportunities for regenerative medicine will be introduced. Signaling and integrative control by the endocrine, autonomic and central nervous systems will be introduced. Prerequisite: Biology or Human Biology core.
Terms: Win
| Units: 4
BIO 214:
Advanced Cell Biology (BIOC 224, MCP 221)
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: 4
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. Satisfies Central Menu Areas 1 or 2. Prerequisite: Biology core.
Terms: Win
| Units: 4
BIO 220:
Essential Mathematics for Research in Life and Social Sciences
Targeted review of mathematics for research in life (and social) sciences. Material includes: real and complex functions, sequences and series, essential calculus, linear algebra, probability, stochastic processes, model-building and introduction to Matlab. Links techniques to applications in research and modeling, particularly in population biology. Students will use online materials including lecture videos, problem sets, course notes, and self-paced tests.
Terms: Win
| Units: 2
BIO 226:
Introduction to Biophysics (APPPHYS 205, BIO 126)
Core course appropriate for advanced undergraduate students and graduate students with prior knowledge of calculus and a college physics course. Introduction to how physical principles offer insights into modern biology, with regard to the structural, dynamical, and functional organization of biological systems. Topics include the roles of free energy, diffusion, electromotive forces, non-equilibrium dynamics, and information in fundamental biological processes.
Terms: Win
| Units: 3-4
BIO 227:
Foundations of Community Ecology
Discussion of classic papers in community ecology (Forbes, Clements, Gleason, Grinnell, Lindeman, Preston, Elton, Hutchinson, May, MacArthur, Odum, Connell, Paine, Tilman, etc.) and contemporary papers on related topics, to develop historical perspectives to understand current issues and identify future directions. Prerequisite for undergraduates: consent of instructor.
| Units: 2
BIO 230:
Molecular and Cellular Immunology
Components of the immune system and their functions in immune responses in health and disease: development of the immune system; innate and adaptive immunity; structure and function of antibodies; molecular biology and biochemistry of antigen receptors and signaling pathways; cellular basis of immune responses and their regulation; genetic control of immune responses and disease susceptibility. Lectures and discussion in class and in sections. Satisfies Central Menu Areas 1 or 2. For upper class undergraduates and graduate students who have not previously taken an introductory immunology course. Prerequisite for undergraduates: Biology or Human Biology core, or consent of instructor.
Terms: Aut
| Units: 4
BIO 230A:
Molecular and Cellular Immunology Literature Review
Special discussion section for graduate students. Supplement to 230. Corequisite: 230.
Terms: Aut
| Units: 1
BIO 232:
Advanced Imaging Lab in Biophysics (APPPHYS 232, BIO 132, BIOPHYS 232, GENE 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
BIO 234:
Conservation Biology: A Latin American Perspective (BIO 144, HUMBIO 112)
Principles and application of the science of preserving biological diversity. Conceptually, this course is designed to explore 4 major components relevant to the conservation of biodiversity, as exemplified by the Latin American region. The conceptual frameworks and principles, however, should be generally applicable, and provide insights for all regions of the world, including those of lesser biodiversity. Satisfies Central Menu Area 4 for Bio majors. Prerequisite: BIO 101, or BIO 43 or HUMBIO 2A with consent of instructor. Graduate level students will be expected to conduct a literature research exercise leading to a written paper, addressing a topic of their choosing, derived from any of the themes discussed in class.
Terms: Spr
| Units: 3
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. Satisfies Central Menu Area 2. Prerequisite: Biology core or consent of instructor. Satisfies WIM in Biology.
Terms: Spr
| Units: 3-4
BIO 23N:
FACEBUG: The Social Life of Microbes
Exploration of three crucial aspects of microbial life. First, examine how the unseen microbial majority is responsible for critical but under-appreciated aspects of the biology of the planet. Second, investigate the array of current genomic and imaging tools available to probe microscopic organisms in the environment. Last, we will research the importance of microbial communities and social dynamics in ecological and human health settings.
| Units: 3
| UG Reqs: GER: DB-NatSci
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. Satisfies Central Menu Areas 1 or 4. Prerequisites: Biology core or graduate standing in any department, and consent of instructor.
Terms: Win
| Units: 4
BIO 249:
The Neurobiology of Sleep (BIO 149, HUMBIO 161)
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.
Last offered: Winter 2013
| 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
| Units: 5
BIO 256:
Epigenetics (BIO 156)
Epigenetics is the process by which phenotypes not determined by the DNA sequence are stably inherited in successive cell divisions. Course will cover the molecular mechanisms governing epigenetics, ranging from the discovery of epigenetic phenomena to present-day studies on the role of chromatin, DNA methylation, and RNA in regulating epigenetics processes. Topics include: position effect gene expression, genome regulation, gene silencing & heterochromatin, histone code, DNA methylation & imprinting, epigenetics & disease, and epigenetic-based therapeutics. Prerequisite: BIO41 and BIO42 or consent of instructor.
Terms: Spr
| Units: 2
BIO 257:
Biochemistry and Molecular Biology of Plants (BIO 157)
Biochemical and molecular basis of plant growth and adaptation. Topics include: hormone signal transduction; photoreceptor chemistry and signaling; metabolite sensing and transport; dynamics of photosynthesis; plant innate immunity and symbiosis. Lectures and readings will emphasize research methods. Prerequisite: Biology core or equivalent, or consent of instructor.
Terms: Spr
| Units: 3-4
BIO 258:
Developmental Neurobiology (BIO 158)
For advanced undergraduates and coterminal students. The principles of nervous system development from the molecular control of patterning, cell-cell interactions, and trophic factors to the level of neural systems and the role of experience in influencing brain structure and function. 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. Satisfies Central Menu Areas 2 or 3. Prerequisite: BIO 42 or equivalent.
Last offered: Spring 2013
| Units: 4
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
| Units: 4
BIO 268:
Statistical and Machine Learning Methods for Genomics (BIOMEDIN 245, CS 373, GENE 245, STATS 166, STATS 345)
Computational algorithms for human genetics research. Topics include: permutation, bootstrap, expectation maximization, hidden Markov model, and Markov chain Monte Carlo. Rationales and techniques illustrated with existing implementations commonly used in population genetics research, disease association studies, and genomics analysis. Prerequisite: GENE 244 or consent of instructor
| Units: 3
BIO 274:
Human Skeletal Anatomy (ANTHRO 175, ANTHRO 275, BIO 174, HUMBIO 180)
Study of the human skeleton (a. k. a. human osteology), as it bears on other disciplines, including medicine, forensics, archaeology, and paleoanthropology (human evolution). Basic bone biology, anatomy, and development, emphasizing hands-on examination and identification of human skeletal parts, their implications for determining an individual¿s age, sex, geographic origin, and health status, and for the evolutionary history of our species. Three hours of lecture and at least three hours of supervised and independent study in the lab each week.
Terms: Win
| Units: 5
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: 3-12
| Repeatable
for credit
BIO 277:
Plant Microbe Interaction (BIO 177)
Molecular basis of plant symbiosis and pathogenesis. Topics include mechanisms of recognition and signaling between microbes and plant hosts, with examples such as the role of small molecules, secreted peptides, and signal transduction pathways in symbiotic or pathogenic interactions. Readings include landmark papers together with readings in the contemporary literature. Prerequisites: Biology core and two or more upper division courses in genetics, molecular biology, or biochemistry. Recommended: plant genetics or plant biochemistry.
Terms: Spr
| Units: 3
BIO 278:
Microbiology Literature (BIO 178)
For advanced undergraduates and first-year graduate students. Critical reading of the research literature in prokaryotic genetics and molecular biology, with particular applications to the study of major human pathogens. Classic and foundational papers in pathogenesis, genetics, and molecular biology; recent literature on bacterial pathogens such as Salmonella, Vibrio, and/or Yersinia. Diverse experimental approaches: biochemistry, genomics, pathogenesis, and cell biology. Prerequisites: Biology Core and two upper-division courses in genetics, molecular biology, or biochemistry.
Terms: Win
| Units: 3
BIO 282:
Modeling Cultural Evolution (BIO 182)
Seminar. Quantitative models for the evolution of socially transmitted traits. Rates of change of learned traits in populations and patterns of cultural diversity as a function of innovation and cultural transmission. Learning in constant and changing environments. Possible avenues for gene-culture coevolution.
Terms: Spr
| Units: 3
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
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. Satisfies Central Menu Area 1 for Bio majors. Prerequisites: CHEM 33, 35, 131, and 135 or 171.
Terms: Aut
| Units: 3
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. Satisfies Central Menu Area 1 for Bio majors. Prerequisite: BIO 188/288 or CHEM 181 or CHEMENG 181/281 (formerly 188/288).
Terms: Win
| Units: 3
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, Sum
| Units: 1-5
| Repeatable
for credit
Instructors: ;
Barton, K. (PI);
Bergmann, D. (PI);
Berry, J. (PI);
Block, B. (PI);
Block, S. (PI);
Boggs, C. (PI);
Crowder, L. (PI);
Cyert, M. (PI);
Daily, G. (PI);
Denny, M. (PI);
Dirzo, R. (PI);
Ehrlich, P. (PI);
Endy, D. (PI);
Feldman, M. (PI);
Fernald, R. (PI);
Field, C. (PI);
Fraser, H. (PI);
Frommer, W. (PI);
Frydman, J. (PI);
Fukami, T. (PI);
Garza, D. (PI);
Gilly, W. (PI);
Gordon, D. (PI);
Gozani, O. (PI);
Grossman, A. (PI);
Hadly, E. (PI);
Hanawalt, P. (PI);
Hekmat-Scafe, D. (PI);
Heller, H. (PI);
Heller, R. (PI);
Jones, P. (PI);
Khalfan, W. (PI);
Khosla, C. (PI);
Klein, R. (PI);
Knope, M. (PI);
Kopito, R. (PI);
Long, S. (PI);
Lowe, C. (PI);
Luo, L. (PI);
Malladi, S. (PI);
McConnell, S. (PI);
Micheli, F. (PI);
Mooney, H. (PI);
Morrison, A. (PI);
Mudgett, M. (PI);
Nelson, W. (PI);
Palumbi, S. (PI);
Petrov, D. (PI);
Red-Horse, K. (PI);
Rosenberg, N. (PI);
Sapolsky, R. (PI);
Schnitzer, M. (PI);
Seawell, P. (PI);
Shatz, C. (PI);
Shen, K. (PI);
Simon, M. (PI);
Simoni, R. (PI);
Skotheim, J. (PI);
Somero, G. (PI);
Stearns, T. (PI);
Thompson, S. (PI);
Tuljapurkar, S. (PI);
Vitousek, P. (PI);
Walbot, V. (PI);
Wang, Z. (PI);
Watanabe, J. (PI);
Watt, W. (PI);
Collins, J. (GP)
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. Taken prior to teaching either of the above courses. May be repeated for credit. Prerequisite: selection by instructor.
Terms: Aut, Win
| Units: 1-2
| Repeatable
for credit
BIO 292:
Curricular Practical Training
CPT course required for international students completing degree requirements.
Terms: Aut, Sum
| Units: 1-3
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: Spr
| Units: 3
BIO 299:
Biology PhD Lab Rotation
Limited to first year Biology PhD students. Lab rotations with Biosciences faculty.
Terms: Aut, Win, Spr, Sum
| Units: 1-10
| Repeatable
for credit
BIO 300:
Graduate Research
For graduate students only. Individual research by arrangement with in-department instructors.
Terms: Aut, Win, Spr, Sum
| Units: 1-10
| Repeatable
for credit
Instructors: ;
Barton, K. (PI);
Bergmann, D. (PI);
Berry, J. (PI);
Block, B. (PI);
Block, S. (PI);
Boggs, C. (PI);
Chen, X. (PI);
Crowder, L. (PI);
Cyert, M. (PI);
Daily, G. (PI);
Denny, M. (PI);
Dinneny, J. (PI);
Dirzo, R. (PI);
Dixon, S. (PI);
Ehrlich, P. (PI);
Feldman, J. (PI);
Feldman, M. (PI);
Fernald, R. (PI);
Field, C. (PI);
Fraser, H. (PI);
Frommer, W. (PI);
Frydman, J. (PI);
Fukami, T. (PI);
Gilly, W. (PI);
Gordon, D. (PI);
Gozani, O. (PI);
Grossman, A. (PI);
Hadly, E. (PI);
Hanawalt, P. (PI);
Heller, H. (PI);
Jones, P. (PI);
Jonikas, M. (PI);
Klein, R. (PI);
Kopito, R. (PI);
Long, S. (PI);
Lowe, C. (PI);
Luo, L. (PI);
McConnell, S. (PI);
Micheli, F. (PI);
Mooney, H. (PI);
Morrison, A. (PI);
Mudgett, M. (PI);
Nelson, W. (PI);
Palumbi, S. (PI);
Peay, K. (PI);
Petrov, D. (PI);
Pritchard, J. (PI);
Red-Horse, K. (PI);
Rosenberg, N. (PI);
Roughgarden, J. (PI);
Sapolsky, R. (PI);
Schnitzer, M. (PI);
Shatz, C. (PI);
Shen, K. (PI);
Simon, M. (PI);
Simoni, R. (PI);
Skotheim, J. (PI);
Somero, G. (PI);
Stearns, T. (PI);
Thompson, S. (PI);
Tsao, P. (PI);
Tuljapurkar, S. (PI);
Vitousek, P. (PI);
Walbot, V. (PI);
Wang, Z. (PI);
Watt, W. (PI);
Collins, J. (GP)
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: 1-10
| Repeatable
for credit
Instructors: ;
Andriacchi, T. (PI);
Barres, B. (PI);
Behr, B. (PI);
Bergmann, D. (PI);
Blau, H. (PI);
Block, B. (PI);
Block, S. (PI);
Boggs, C. (PI);
Boothroyd, J. (PI);
Brown, J. (PI);
Brown, P. (PI);
Brunet, A. (PI);
Brunger, A. (PI);
Brutlag, D. (PI);
Burgos, T. (PI);
Butcher, E. (PI);
Butte, A. (PI);
Chan, P. (PI);
Chen, J. (PI);
Cimprich, K. (PI);
Clandinin, T. (PI);
Cleary, M. (PI);
Cochran, J. (PI);
Contag, C. (PI);
Crabtree, G. (PI);
Crowder, L. (PI);
Cyert, M. (PI);
Daily, G. (PI);
Davis, M. (PI);
Davis, R. (PI);
Denny, M. (PI);
Diehn, M. (PI);
Dirzo, R. (PI);
Du Bois, J. (PI);
Ehrhardt, D. (PI);
Ehrlich, P. (PI);
Eliashberg, Y. (PI);
Fathman, C. (PI);
Feldman, M. (PI);
Felsher, D. (PI);
Fernald, R. (PI);
Field, C. (PI);
Fire, A. (PI);
Ford, J. (PI);
Fraser, H. (PI);
Fredericson, M. (PI);
Freyberg, D. (PI);
Frommer, W. (PI);
Frydman, J. (PI);
Fukami, T. (PI);
Fuller, M. (PI);
Gardner, C. (PI);
Garner, C. (PI);
Gilly, W. (PI);
Glenn, J. (PI);
Gold, G. (PI);
Goodman, M. (PI);
Goodman, S. (PI);
Gordon, D. (PI);
Gozani, O. (PI);
Hadly, E. (PI);
Hanawalt, P. (PI);
Haskell, W. (PI);
Heilshorn, S. (PI);
Heller, H. (PI);
Helms, J. (PI);
Herzenberg, L. (PI);
Hsu, S. (PI);
Jones, P. (PI);
Katzenstein, D. (PI);
Kay, M. (PI);
Khalfan, W. (PI);
Khavari, P. (PI);
Kim, S. (PI);
Klein, R. (PI);
Knope, M. (PI);
Koong, A. (PI);
Kopito, R. (PI);
Kornberg, A. (PI);
Krams, S. (PI);
Kuo, C. (PI);
Launer, A. (PI);
Lee, P. (PI);
Levy, R. (PI);
Lin, M. (PI);
Long, S. (PI);
Longaker, M. (PI);
Lowe, C. (PI);
Luo, L. (PI);
Lyons, D. (PI);
MacIver, M. (PI);
Maduke, M. (PI);
Maldonado, Y. (PI);
Malenka, R. (PI);
Marinkovich, M. (PI);
Matheson, G. (PI);
McConnell, S. (PI);
Micheli, F. (PI);
Mignot, E. (PI);
Miklos, D. (PI);
Mochly-Rosen, D. (PI);
Monack, D. (PI);
Montgomery, S. (PI);
Mooney, H. (PI);
Morris, R. (PI);
Morrison, A. (PI);
Mudgett, M. (PI);
Murphy, G. (PI);
Mustapha, M. (PI);
Naumovski, L. (PI);
Nayak, N. (PI);
Nelson, W. (PI);
Nishino, S. (PI);
Nolan, G. (PI);
Nusse, R. (PI);
Oro, A. (PI);
Palmer, T. (PI);
Palumbi, S. (PI);
Parker, K. (PI);
Petrov, D. (PI);
Pollack, J. (PI);
Pringle, J. (PI);
Rando, T. (PI);
Raymond, J. (PI);
Red-Horse, K. (PI);
Reijo Pera, R. (PI);
Reimer, R. (PI);
Relman, D. (PI);
Robinson, B. (PI);
Rockson, S. (PI);
Rohatgi, R. (PI);
Root, T. (PI);
Rosenberg, N. (PI);
Rothschild, L. (PI);
Sage, J. (PI);
Sapolsky, R. (PI);
Scherrer, G. (PI);
Schnitzer, M. (PI);
Scott, M. (PI);
Shapiro, L. (PI);
Shatz, C. (PI);
Shen, K. (PI);
Sherlock, G. (PI);
Shooter, E. (PI);
Shrager, J. (PI);
Shulman, N. (PI);
Sibley, E. (PI);
Sikic, B. (PI);
Simon, M. (PI);
Simoni, R. (PI);
Singh, U. (PI);
Skirboll, S. (PI);
Skotheim, J. (PI);
Somero, G. (PI);
Sonnenburg, J. (PI);
Spormann, A. (PI);
Spudich, J. (PI);
Stearns, T. (PI);
Steinman, L. (PI);
Sudhof, T. (PI);
Sun, Z. (PI);
Sweet-Cordero (PI);
Tan, M. (PI);
Theriot, J. (PI);
Thompson, S. (PI);
Triadafilopoulos, G. (PI);
Tsao, P. (PI);
Tuljapurkar, S. (PI);
Umetsu, D. (PI);
Vemuri, M. (PI);
Vitousek, P. (PI);
Walbot, V. (PI);
Watt, W. (PI);
Waymouth, R. (PI);
Weissman, I. (PI);
West, R. (PI);
Wong, A. (PI);
Wu, J. (PI);
Wysocka, J. (PI);
Yang, F. (PI);
Yang, Y. (PI);
Yao, M. (PI);
Zarins, C. (PI);
Zhao, H. (PI);
de Lecea, L. (PI);
Collins, J. (GP);
Kuhn, R. (GP)
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: 1-3
| Repeatable
for credit
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. This course isnnopen only to Biology PhD students and is not open to auditors."
Terms: Aut
| Units: 1
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. This course isnnopen only to Biology PhD students and is not open to auditors."
Terms: Win
| Units: 1
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. This course isnnopen only to Biology PhD students and is not open to auditors.
Terms: Spr
| Units: 1
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
BIO 31Q:
Ants: Behavior, Ecology, and Evolution
Preference to sophomores. Behavior: the organization of colonies, how they operate without central control, how they resemble other complex systems like brains. Ecology: how populations of colonies change, comparing the ecology of a species in SW American desert and invasive Argentine ants. Evolution: why are there so many species of ants; how are they alike, how do they differ, and why? Ants as the theme for exploring how to do research in animal behavior, ecology, and evolution. Research project will be on the invasive Argentine ant: its distribution on campus, foraging trails, and nest structure.
| Units: 3
BIO 325:
The Evolution of Body Size (GES 325)
Preference to graduate students and upper-division undergraduates in GES and Biology. 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?
| Units: 2
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: 1-3
| Repeatable
for credit
BIO 346:
Advanced Seminar on Prokaryotic Molecular Biology
Enrollment limited to PhD students associated with departmental research groups in genetics or molecular biology.
Terms: Aut, Win
| Units: 1
BIO 375:
Field Ecology & Conservation
This course is based on question-driven research in the field, addressing both conceptual frameworks and methodological aspects of evolutionary ecology and conservation biology. It consists of faculty-led research projects and student independent projects. The field part takes place in a tropical rain forest research station in Mexico September 5-15, 2014. The field component is followed by sessions on campus, where the research data are analyzed, discussed and prepared as scientific papers. The training includes presentations of the papers in a mini-symposium organized as a professional meeting.
Terms: Aut
| Units: 4
BIO 37N:
Green Revolution and Plant Biotechnology
Feeding ever-growing populations is a constant challenge to mankind. In the second half of the 20th century, the breeding of improved varieties combined with the use of chemical fertilizers and pesticides led to crop yield increases labeled the Green Revolution. Modern technologies in genetic engineering are expected to bring the second green revolution. Meeting the current and future global food needs without further damaging the fragile environment requires innovative effort from scientists and the society.
| Units: 3
| UG Reqs: GER: DB-NatSci
BIO 383:
Seminar in Population Genetics
Literature review, research, and current problems in the theory and practice of population genetics and molecular evolution. May be repeated for credit. Prerequisite: consent of instructor.
Terms: Aut, Win, Spr
| Units: 1-3
| Repeatable
for credit
BIO 387:
Hacking Consciousness: Consciousness, Cognition, and the Brain
Listen to renowned physicists, nutritionists, neuroscientists, etc. as they investigate the nature of consciousness as a field of all possibilities. We'll explore consciousness as the source not only of the human mind and its ability to experience, know, innovate... but also as the source of all structures and functions in creation, from fine particles to DNA to galaxies, in parallel with the scientific notion of a unified field, or superstring at the basis of the infinite diversity of time and space.
Terms: Spr
| Units: 1
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
| Repeatable
for credit
BIO 802:
TGR Dissertation
Terms: Aut, Win, Spr, Sum
| Units: 0
| Repeatable
for credit
Instructors: ;
Baker, B. (PI);
Barton, K. (PI);
Bergmann, D. (PI);
Berry, J. (PI);
Block, B. (PI);
Block, S. (PI);
Boggs, C. (PI);
Crowder, L. (PI);
Cyert, M. (PI);
Daily, G. (PI);
Denny, M. (PI);
Dirzo, R. (PI);
Ehrlich, P. (PI);
Epel, D. (PI);
Feldman, M. (PI);
Fernald, R. (PI);
Field, C. (PI);
Fraser, H. (PI);
Frommer, W. (PI);
Frydman, J. (PI);
Fukami, T. (PI);
Gilly, W. (PI);
Gordon, D. (PI);
Gozani, O. (PI);
Grossman, A. (PI);
Hadly, E. (PI);
Hanawalt, P. (PI);
Heller, H. (PI);
Jones, P. (PI);
Klein, R. (PI);
Kopito, R. (PI);
Long, S. (PI);
Lowe, C. (PI);
Luo, L. (PI);
McConnell, S. (PI);
Micheli, F. (PI);
Mooney, H. (PI);
Morrison, A. (PI);
Mudgett, M. (PI);
Nelson, W. (PI);
Palumbi, S. (PI);
Peay, K. (PI);
Petrov, D. (PI);
Red-Horse, K. (PI);
Rosenberg, N. (PI);
Roughgarden, J. (PI);
Sapolsky, R. (PI);
Schnitzer, M. (PI);
Shatz, C. (PI);
Shen, K. (PI);
Simon, M. (PI);
Simoni, R. (PI);
Skotheim, J. (PI);
Somero, G. (PI);
Stearns, T. (PI);
Thompson, S. (PI);
Tuljapurkar, S. (PI);
Vitousek, P. (PI);
Walbot, V. (PI);
Wang, Z. (PI);
Watt, W. (PI);
Wong, W. (PI);
Collins, J. (GP)
BIO 102:
Demography: Health, Development, Environment (HUMBIO 119)
Demographic methods and their application to understanding and projecting changes in human infant, child, and adult mortality and health, fertility, population, sex ratios, and demographic transitions. Progress in human development, capabilities, and freedoms. Relationships between population and environment. Prerequisites: numeracy and basic statistics; Biology or Human Biology core; or consent of instructor.
| Units: 3
| UG Reqs: GER:DB-SocSci
BIO 106:
Human Origins (ANTHRO 6, ANTHRO 206, HUMBIO 6)
The human fossil record from the first non-human primates in the late Cretaceous or early Paleocene, 80-65 million years ago, to the anatomically modern people in the late Pleistocene, between 100,000 to 50,000 B.C.E. Emphasis is on broad evolutionary trends and the natural selective forces behind them.
| Units: 5
| UG Reqs: GER: DB-NatSci
BIO 119:
Physiology of Global Change
Increased emissions of greenhouse gases into the atmosphere are inducing drastic shifts in many environmental factors. How will these environmental changes affect organisms and the ecosystems in which they occur? Are some species more vulnerable to global change than others? Examining how shifts in abiotic factors affect organismal physiology offers a powerful mechanistic tool to better understand species¿ responses to global change. This seminar will focus on the physiological stress resulting from and the adaptive responses made to changes in temperature, salinity, dissolved oxygen, and ocean acidity in a range of species with an emphasis on marine organisms. Interactions among these abiotic factors will show that an integrative physiological analysis is required to develop a mechanistic understanding of effects of global change. The course will be based on short lectures followed by discussions of relevant primary literature. Guest speakers will bring in special expertise on several key issues. The course will include a field trip to Hopkins Marine Station.
| Units: 1
BIO 127:
From Generation to Generation: Scientific and Cultural Approaches to Jewish Genetics
This series of guest lectures aims to explore the connections between genetics and Jewish Studies. How do different Jewish populations relate to each other? To what extent are Jewish populations of the present descended from those of the past? What are the causes of diseases that occur disproportionately in Jewish populations? These and other questions will be addressed in a program that crosses the boundaries between science and Jewish Studies, culture and biology.
| Units: 1
BIO 138:
Ecosystem Services: The Science of Valuing Nature (BIO 238)
This advanced course explores the science of valuing nature, beginning with its historical origins, and then its recent development in natural (especially ecological), economic, psychological, and other social sciences. We will use the ecosystem services framework (characterizing benefits from ecosystems to people) to define the state of knowledge, core methods of analysis, and research frontiers, such as at the interface with biodiversity, resilience, human health, and human development. Intended for diverse students, with a focus on research and real-world cases. Class size is limited to 12. To apply, please email the instructor (gdaily@stanford.edu) with a brief description of your background and research interests.
| Units: 3
BIO 143:
Evolution
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. Satisfies Central Menu Area 4.
| Units: 3
| UG Reqs: GER: DB-NatSci
BIO 145:
Behavioral Ecology (BIO 245)
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. Satisfies Central Menu Area 4 for Bio majors. Prerequisites: Biology or Human Biology core, or consent of instructor. Recommended: statistics. Satisfies WIM in Biology.
| Units: 4
| UG Reqs: GER: DB-NatSci
BIO 152:
Imaging: Biological Light Microscopy (MCP 222)
Survey of instruments which use light and other radiation for analysis of cells in biological and medical research. Topics: basic light microscopy through confocal fluorescence and video/digital image processing. Lectures on physical principles; involves partial assembly and extensive use of lab instruments. Lab. Prerequisites: some college physics, Biology core.
| Units: 3
| UG Reqs: GER: DB-NatSci
BIO 163:
Neural Systems and Behavior (BIO 263, 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. Satisfies Central Menu Area 3 for Bio majors. Prerequisites: BIO 42, HUMBIO 4A.
| Units: 4
| UG Reqs: GER: DB-NatSci
BIO 164:
Biosphere-Atmosphere Interactions (BIO 264)
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.
| Units: 4
| UG Reqs: GER: DB-NatSci
BIO 166:
Faunal Analysis: Animal Remains for the Archaeologist (ANTHRO 113, ANTHRO 213, BIO 266)
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.
| Units: 5
BIO 171:
Principles of Cell Cycle Control (BIO 271, CSB 271)
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. Satisfies Central Menu Area 2.
| Units: 3
| UG Reqs: GER: DB-NatSci
BIO 172:
Molecular Basis of Body Plan Evolution (BIO 272)
Developmental biology research, from arthropods and chordates, over the past 25 years has revealed astonishing levels of shared developmental similarities, despite large morphological differences between the two groups, and has led to speculation about the morphology of the earliest animals. This has led to a synthesis between developmental biology, zoology, and paleontology and sparked molecular developmental studies in diverse metazoan phyla. Focus is on the latest findings from comparative development and what they reveal about the early evolution of the animal phyla.
| Units: 4
BIO 175:
Tropical Ecology and Conservation
Spring Break trip to a field station; lectures at Stanford. How to address scientific questions concerning ecology and conservation. Field trip includes natural history observations and group research projects. Symposium based on project results.
| Units: 5
| UG Reqs: GER: DB-NatSci
BIO 186:
Natural History of the Vertebrates (BIO 286)
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.
| Units: 4
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.
| Units: 3
BIO 216:
Terrestrial Biogeochemistry (EESS 216)
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.
| 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.
| Units: 4
BIO 221:
Methods of Theoretical Population Biology
Formulation and analysis of problems in population biology using theoretical and computational numerical methods. Topics include deterministic and stochastic models, structured populations, stability and bifurcations, and data-driven models with applications in ecology and genetics. Prerequisites: Bio 220 or consent of instructor.
| Units: 4
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 and graduate students with background in physical science, engineering, and biology may apply to enroll. Recommended: background in neuroscience.
| 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.
| Units: 3
BIO 238:
Ecosystem Services: The Science of Valuing Nature (BIO 138)
This advanced course explores the science of valuing nature, beginning with its historical origins, and then its recent development in natural (especially ecological), economic, psychological, and other social sciences. We will use the ecosystem services framework (characterizing benefits from ecosystems to people) to define the state of knowledge, core methods of analysis, and research frontiers, such as at the interface with biodiversity, resilience, human health, and human development. Intended for diverse students, with a focus on research and real-world cases. Class size is limited to 12. To apply, please email the instructor (gdaily@stanford.edu) with a brief description of your background and research interests.
| Units: 3
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. Satisfies Central Menu Area 4 for Bio majors. Prerequisites: Biology or Human Biology core, or consent of instructor. Recommended: statistics. Satisfies WIM in Biology.
| Units: 4
BIO 254:
Molecular and Cellular Neurobiology (NBIO 254)
For graduate students. Includes lectures for BIO 154. 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.
| Units: 5
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. Satisfies Central Menu Area 3 for Bio majors. Prerequisites: BIO 42, HUMBIO 4A.
| Units: 4
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.
| Units: 4
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.
| Units: 5
BIO 271:
Principles of Cell Cycle Control (BIO 171, CSB 271)
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. Satisfies Central Menu Area 2.
| Units: 3
| UG Reqs: GER: DB-NatSci
BIO 272:
Molecular Basis of Body Plan Evolution (BIO 172)
Developmental biology research, from arthropods and chordates, over the past 25 years has revealed astonishing levels of shared developmental similarities, despite large morphological differences between the two groups, and has led to speculation about the morphology of the earliest animals. This has led to a synthesis between developmental biology, zoology, and paleontology and sparked molecular developmental studies in diverse metazoan phyla. Focus is on the latest findings from comparative development and what they reveal about the early evolution of the animal phyla.
| Units: 4
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.
| Units: 4
BIO 287:
Advanced topics in human population genetics
Focused examination of specific topics in human population genetics, with emphasis on primary literature. Course themes may include: mathematical properties of statistics used in human population genetics, population genetics and ¿biological race,¿ and statistical inference of human migrations.
| Units: 3
BIO 306:
Current Topics in Integrative Organismal Biology
Limited to and required of graduate students doing research in this field. At Hopkins Marine Station.
| Units: 1
BIO 321:
Ecological Genetics
Systematic exploration of (1) the types of questions that can be addressed by ecological genetics techniques (i.e., community genomics, genetic variation between species in the same ecosystem, resource use, landscape genetics, etc.); (2) laboratory techniques available; and (3) analyses and modeling best suited for ecological genetics questions. Analysis of specific research problems and efforts (now underway or planned for the near future) among seminar participants, and discussion of these efforts with group review of the relative merits of alternative approaches.
| Units: 1-3
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.
| Units: 1-2
| Repeatable
for credit
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.
| Units: 4
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.
| Units: 2
BIO 384:
Theoretical Ecology
Recent and classical research papers in ecology, and presentation of work in progress by participants. Prerequisite: consent of instructor.
| Units: 1-3
| Repeatable
for credit
BIO 390:
Topics in Biology
Seminar. Topics in biology ranging from neurobiology to ecology.
| Units: 1
