BIO 2N:
Ecology and Evolution of Infectious Disease in a Changing World
This seminar will explore the ways in which anthropogenic change, climate change, habitat destruction, land use change, and species invasions effects the ecology and evolution of infectious diseases. Topics will include infectious diseases of humans, wildlife, livestock, and crops, effects of disease on threatened species, disease spillover, emerging diseases, and the role of disease in natural systems. Course will be taught through a combination of popular and scientific readings, discussion, and lecture. .
Terms: Spr
| Units: 3
| UG Reqs: WAY-SMA
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.
Terms: Spr
| Units: 3
| UG Reqs: GER: DB-NatSci
BIO 4N:
Peopleomics: The science and ethics of personalized genomic medicine
Exploration of the new field of personalized genomic medicine. Personalized medicine is based on the idea that each person's unique genome sequence can be used to predict risk of acquiring specific diseases, and to make more informed medical choices. The science behind these approaches; where they are heading in the future; and the ethical implications such technology presents. Lectures augmented with hands-on experience in exploring and analyzing a real person's genome.
| Units: 3
| UG Reqs: GER: DB-NatSci
BIO 5N:
Tipping Point for Planet Earth: How Close Are We to the Edge?
We will explore why the earth is headed toward a tipping point: a change that is so rapid, so extreme, and so unexpected that humanity may not be able to recover. We will cover synergies between people, stuff, storms, hunger, thirst, toxins, disease and war. Students will read chapters from the instructor¿s new book, Tipping Point for Planet Earth, and will participate in class discussions. Each student will produce their own projects based on one of the course themes.
Terms: Aut
| Units: 3
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 optional 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
Introduction to several major fields of biology, including biochemistry, cell biology, genetics, evolution, and biodiversity. Introduces the general approaches used by scientists to study life and explores recent advances in each area during weekly discussion section. Not intended for biology majors, but provides the foundation for higher-level biology courses. Prerequisite: high school biology.
Terms: Sum
| Units: 3
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 7SL:
Introduction to Biology Lab
Optional laboratory to be taken with BIO7S. Introduction to basic biological laboratory techniques, including microscopy, identification of biomolecules, assaying enzyme activity, genetic manipulation of microorganisms, assaying the effects of gene mutation on protein function, and using PCR to genotype organisms.
Last offered: Summer 2016
| Units: 2
BIO 8N:
Human Evolution
A survey of the anatomical and behavioral evidence for human evolution and of the increasingly important information from molecular genetics. Emphasis on the split between the human and chimpanzee lines 6-7 million years ago, the appearance of the australopiths by 4.1 million years ago, the emergence of the genus Homo about 2.5 million years ago, the spread of Homo from Africa 1.7-1.6 million years ago, the subsequent divergence of Homo into different species on different continents, and the expansion of fully modern humans (Homo sapiens) from Africa about 50,000 years ago to replace the Neanderthals and other non-modern Eurasians.
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.
Last offered: Autumn 2011
| Units: 2
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. We will conduct investigations across all of these contexts toward an inclusive understanding of ¿place¿, ultimately to lead us to explore our own lives in relation to the natural world, historical and cultural milieu, and the direction of our individual life path.n The location at the entry point to the Big Sur Coast of California provides a unique outdoor laboratory in which to study the biology of the bay and the adjacent coastal lands. It is also an area with a deep cultural, literary and artistic history. We will meet marine biologists, experts in the literary history of Cannery Row and the writings of John Steinbeck, local artists and photographers, experts in the neuroscience of creativity, as well as people who are very much involved in the forces and fluxes that steer modern culture. This rich and immersive approach provides students a rare opportunity to reflect on their relationships to nature, culture, and their own individual goals.nThe course emphasizes interactions and discussions. We will be together all of the time, either at our base at the Belden House in Pacific Grove, hiking and camping in Big Sur¿s pristine Big Creek Reserve on the rocky coast, and traveling to the Tassajara Mountain Zen Center in the Ventana wilderness for several days. This is not an ordinary academic experience, instead it is an adventure of a personal, intellectual, spiritual and physical kind. We welcome people with wide interests; artists, poets, writers, engineers, scientists and musicians. Mostly we invite people with an open mind and a sense of adventure. nStudents 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.n Note: 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 to campus on Monday, September 4 (Labor Day). Transportation to campus from the Belden House in Pacific Grove will be provided on Saturday, September 23.
Terms: Sum
| Units: 2
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 16:
Conservation Storytelling: Pre-course for BOSP South Africa
Limited to students admitted to the BOSP South Africa overseas seminar. Through 4 workshop meetings, students will develop and pitch story ideas, form teams in which a writer and a photographer agree to collaborate on a story, and conduct background research prior to departing for South Africa.
Last offered: Spring 2016
| Units: 1
BIO 24N:
Visions of Paradise: Garden Design
Through literature readings and field trips to local gardens learn the principles and esthetics of classic garden designs: Italian Renaissance, botanical teaching, Japanese, English cottage, and others. Design a personal vision of paradise with details of species, visual and scent impact, water features, and hardscape. Open your eyes to a new appreciation of the world of plants and learn some physiology and genetics that explains the specific properties of individual species.
Terms: Spr
| Units: 3
BIO 25Q:
The Molecular Basis of Genetic Disease
Preference to sophomores. Focus is on two genetic diseases resulting from the production of protein molecules that are unable to fold into their native conformations, called conformational diseases: cystic fibrosis and amyotrophic lateral sclerosis or Lou Gehrig's disease. Hypotheses and controversies surrounding the molecular basis of these disorders, and implications for novel therapeutics. Readings from research literature.
Last offered: Spring 2016
| Units: 3
| UG Reqs: GER: DB-NatSci, WAY-SMA
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: Win
| Units: 3
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 26S:
Maintenance of the Genome
The precious blueprint for life is entrusted to genome maintenance proteins found in all living cells. This seminar introduces the remarkable systems that scan cellular DNA for alterations and make repairs to ensure genomic stability. We further explore how deficiencies in these systems can lead to developmental defects, premature aging, and predisposition to cancer. Course includes background reading from primary articles, introductory lectures, student presentations, and a short term paper. Prerequisites: High school Biology. Preference to Stanford students.
Terms: Sum
| Units: 3
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 32Q:
Neuroethology: The Neural Control of Behavior (HUMBIO 91Q)
Preference to sophomores. Animal behavior offers insights about evolutionary adaptations and this seminar will discuss the origins of the study of animal behavior and its development to the present. How does the nervous system control behavior and how is it changed by behavior? We will analyze and discuss original research papers about the neural basis of behavior. The use and misuse of parallels between animal and human behavior. Possible field trip to observe animals in their natural habitat.
Terms: Win
| Units: 3
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 33N:
Conservation Science and Practice
Preference to freshmen. This course will explore the potential for harmonizing people and nature, for achieving improved outcomes in the well-being of both as a result of conservation investments and interventions. We will consider biophysical, economic, social, and psychological perspectives, examining an array of conservation goals, from protecting endangered species to securing ecosystem services (such as flood control and climate stability) to alleviating poverty and improving mental well-being. We will also study the design and implementation of real conservation and human development efforts worldwide, among the many farmers, ranchers, fishing people, and others managing Earth's lands and waters. Highlights include a field trip to Jasper Ridge Biological Preserve, Stanford¿s very own nature reserve, and guest visits of some impressive conservation leaders internationally.
Terms: Spr
| 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.
Last offered: Autumn 2015
| 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 41A:
Bio Solve-It
Students enrolled in Bio41 lecture and regular discussion sections attend two additional 80 min sections per week. The objective of the course is to help students to solidify basic concepts, identify areas to work on, and apply core concepts learned that week in Bio41 lecture and section. Space is limited, by application only. Co-Requisite: Bio 41.
Terms: Aut
| Units: 1
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 2015
| 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 42A:
Bio Solve-It
Students enrolled in Bio42 lecture and regular discussion sections attend two additional 80 min sections per week. The objective of the course is to help students to solidify basic concepts, identify areas to work on, and apply core concepts learned that week in Bio42 lecture and section. Space is limited, by application only. Co-Requisite: Bio 42.
Terms: Win
| Units: 1
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 43A:
Bio Solve-It
Students enrolled in Bio43 lecture and regular discussion sections attend two additional 80 min sections per week. The objective of the course is to help students to solidify basic concepts, identify areas to work on, and apply core concepts learned that week in Bio43 lecture and section. Space is limited, by application only. Co-Requisite: Bio 43.
Terms: Spr
| Units: 1
BIO 45:
Introduction to Laboratory Research in Cell and Molecular Biology
Investigate yeast strains that are engineered to express the human tumor suppressor 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 Guardian of the Genome through lectures and by reading and discussing journal articles. Use molecular visualization programs to examine the structure of normal and mutant p53 proteins. Assay the ability of mutant p53 to direct expression of several reporter genes. During guided reflection, investigate further and identify what could be wrong with the p53 mutants you have been studying. Conduct lab experiments to test hypotheses, analyze data, and present your findings through a team oral presentation, as well as a scientific poster. There are no pre-requisites for this course. However, having taken CHEM 31X, or 31A and B, and 33 and being concurrently enrolled or past enrollment in Biology or Human Biology core will help. Note: This class has a $25 course fee. More information can be found at http://web.stanford.edu/class/bio45
Terms: Aut, Win
| Units: 4
| UG Reqs: WAY-SMA
Instructors: ;
Cyert, M. (PI);
Hekmat-Scafe, D. (PI);
Imam, J. (PI);
Malladi, S. (PI);
Stearns, T. (PI);
Bump, P. (TA);
Conlon, M. (TA);
Flores Servin, J. (TA);
Forcina, G. (TA);
Li, J. (TA);
Perez, B. (TA);
Persson, L. (TA);
Tran, M. (TA)
BIO 46:
Introduction to Research in Ecology and Evolutionary Biology
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 writing and sharing results. To build these skills, this course focuses on the microorganisms associated with lichen epiphytes. Students, working in teams, develop novel research hypotheses and execute the necessary experiments and measurements to test these hypotheses. In addition, students will learn how to manipulate, visualize and analyze data in R. The capstone of the course is an oral defense of students' findings, as well as a research paper in the style of a peer-reviewed journal article. Labs are completed both on campus and at Jasper Ridge. Lab fee. Information about this class is available at http://bio44.stanford.edu. Satisfies WIM in Biology.
Terms: Win
| Units: 4
| UG Reqs: WAY-SMA
BIO 47:
Introduction to Research in Ecology and Evolutionary Biology
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 nectar microbes 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. Satisfies WIM in Biology.
Terms: Spr
| Units: 4
BIO 50S:
Introduction to Cancer Biology
Introduction to the molecular basis of cancer. This course will examine the biological processes that are disrupted in cancer, such as DNA repair, cell cycle control and signaling pathways, as well as the science behind some current treatments. Prerequisites: general biology
Last offered: Summer 2016
| Units: 3
BIO 51S:
The Gene: The History and Science of our Genetic Code
This discussion-based course will use the novel ¿The gene¿ by Siddhartha Mukherjee and other selected readings to explore the science behind our genetic code. We will cover topics such as regulation of gene expression, inheritance, genetic testing, manipulation of the genome, and the relationship between genetics and identity. Prerequisites: Instructor consent, AP Biology Recommended.
Terms: Sum
| Units: 3
BIO 52:
I, Biologist: Diversity Improves the Science of Biology (CSRE 52H)
Disciplinary priorities, research agendas, and innovations are determined by the diversity of participants and problem-solving is more successful with a broad range of approaches. Using case studies in biological research, we propose to use these insights to help our students learn why a diverse scientific community leads to better discovery and improves the relevance of science to society. Our premise is that a diverse set of perspectives will impact not only how we learn science, but how we do science.
Terms: Spr
| Units: 1
BIO 60:
Introduction to Problem Solving in Biology
Why is Lyme disease spreading? How does HIV become drug resistant? How do other animals affect our disease risk? In BIO 60 students will examine actual case studies to experience how different scientific approaches are used to battle infectious disease. They will evaluate information presented in the popular media and the scientific literature, and will directly participate in the scientific process through hands-on collection, documentation and analyses of authentic scientific data. Students will cultivate their scientific curiosity by discovering the natural world with a Foldscope, the `origami paper microscope¿ (https://microcosmos.foldscope.com). Students will build critical thinking skills by creating hypotheses, and designing experiments that pertain to problems in infectious disease. Students will work in teams to expand their thinking and will practice communicating science to different audiences.
Terms: Spr
| Units: 4
| UG Reqs: WAY-SMA
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 (HUMBIO 136)
This laboratory course is active and inquiry based. Aspects of exercise and temperature are explored; however, the specific questions the class tackles differ each quarter. Samples of past questions: Does lactic acid accumulation correlate with exercise fatigue at different exercise and body temperatures? Does palm cooling during exercise mitigate the effect of body temperature on fatigue with or without evaporative cooling? Students participate both as experimenters and as subjects of the experiments in two-person teams. Participants must be in good physical condition, though not necessarily athletes, and must be willing to participate in strenuous exercise routines under adverse environmental conditions. Varsity athletes concurrently participating in a spring sport must consult the instructor before applying. Discussion sessions include student presentations of journal articles, data analyses, and feedback on individual WIM research proposals. By application only, see sites.stanford.edu/bio107humbio136 for the application form. Prerequisite: Bio 42 or HumBio 4A. Satisfies WIM for Biology.
Terms: 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 and related areas. The course will teach and use the computer language R and Python (you learn both, choose one). Topics include distributions, probabilities, likelihood, linear models; illustrations will be based on recent research.
Last offered: Spring 2016
| Units: 4
| UG Reqs: WAY-AQR
BIO 109A:
The Human Genome and Disease (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 (BIOC 109B)
Continuation of 109A/209A. Genetic drift: the path of human predecessors out of Africa to Europe and then either through Asia to Australia or through northern Russia to Alaska down to the W. Coast of the Americas. Support for this idea through the histocompatibility genes and genetic sequences that predispose people to diseases. Guest lectures from academia and pharmaceutical companies. Prerequisite: Biology or Human Biology core. 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 110:
Chromatin Regulation of the Genome (BIO 210)
Maintenance of the genome is a prerequisite for life. In eukaryotes, all DNA-templated processes are tightly connected to chromatin structure and function. This course will explore epigenetic and chromatin regulation of cellular processes related to aging, cancer, stem cell pluripotency, metabolic homeostasis, and development. Course material integrates current literature with a foundational review of histone modifications and nucleosome composition in epigenetic inheritance, transcription, replication, cell division and DNA damage responses. Prerequisite: BIO 41 or consent of instructor.
Terms: Aut
| Units: 3
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 112:
Human Physiology (HUMBIO 133)
Human physiology will be examined by organ systems: cardiovascular, respiratory, renal, gastrointestinal and endocrine. Molecular and cell biology and signaling principles that underlie organ development, pathophysiology and opportunities for regenerative medicine are discussed, as well as integrative control mechanisms and fetal development. 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 115:
The Hidden Kingdom - Evolution, Ecology and Diversity of Fungi (BIO 239)
Fungi are critical, yet often hidden, components of the biosphere. They regulate decomposition, are primary partners in plant symbiosis and strongly impact agriculture and economics. Students will explore the fascinating world of fungal biology, ecology and evolution via lecture, lab, field exercises and Saturday field trips that will provide traditional and molecular experiences in the collection, analysis and industrial use of diverse fungi. Students will chose an environmental niche, collect and identify resident fungi, and hypothesize about their community relationship. Prerequisite: Bio 43 recommended.
Last offered: Winter 2016
| Units: 4
| UG Reqs: WAY-SMA
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.
Terms: Aut
| Units: 4
| UG Reqs: GER: DB-NatSci
BIO 117:
Biology and Global Change (EARTHSYS 111, ESS 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
Focus is on using mutations and genetic analysis to study biological and medical questions. The first portion of the course covers how the identification and analysis of mutations can be used in model systems to investigate biological processes such as development and metabolism. In the second portion of the course, we focus on the use of existing genetic variation in humans and other species to identify disease-associated genes as well as to investigate variation in morphological traits such as body size and shape.
Terms: Aut
| 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.
Last offered: Spring 2014
| Units: 3
BIO 123A:
Cell and Developmental Biology I
This is the first of a two course series that explores organizing principles of development at the cellular and tissue level. Students will learn the mechanisms by which cells polarize, interact with each other and their environment, divide, and generate force and movement and how these processes are utilized during the development of multicellular organisms. The course will also cover how cells communicate to pattern cell specification and morphogenesis during tissue and organ formation and during stem cell regulated homeostasis.
Terms: Aut
| Units: 4
BIO 124:
Topics in Cancer Biology
This discussion-based course will explore the scientific tools used to study the molecular and genetic basis of cancer and to develop treatments for this disease. Topics covered may include cancer models, traditional and targeted cancer therapies, and the development of resistance to treatment. Students will develop skills in critical reading of primary research articles and will also complete a final project. Prerequisites: Biology/Human Biology core or equivalent or consent of instructor.
Terms: Spr
| Units: 3
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 131:
Complex Systems Lab
Applications of complex systems will be explored in thisnseminar through lectures, discussions, and a class project. Lecture topicsninclude a discussion of chaos in weather modeling and aircraft turbulence,napplication of network science to understand Ebola and the ALS ice bucketnchallenge, and self-organized processes such as crowd dynamics andnWikipedia. The first half of the course will emphasize complex systemsnapplications. Students will apply complex systems analysis techniques tontheir personal research, a current event, or repeat a classic complexnsystems experiment. Projects can include topics such as calculating thenfractal dimension of a forest, simulating crowd dynamics, studying thendegree distribution of social networks, or making a Van der Pol oscillator.nGraduate student led seminar. Can be repeated for credit.
Terms: Win
| 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, microendoscopy, 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 137:
Plant Genetics
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 138:
Ecosystem Services: Frontiers in 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. To apply, please email the instructor (gdaily@stanford.edu) with a brief description of your background and research interests.
Terms: Aut
| Units: 3
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 143:
Evolution
Principles of evolution. Adaptation and natural selection. Darwin and the history of evolutionary thought. Population genetics, including genetic variation and mutation, and effects of migration, drift, linkage, and recombination. Evolutionary phenomena: developmental evolution, life history evolution, molecular evolution, sexual selection, social evolution, and speciation. Pattern and process in biological diversity. Case studies, including human evolution. Satisfies central menu area 4, ecology & evolution.
Terms: Win
| Units: 3
| UG Reqs: GER: DB-NatSci
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 145:
Ecology and Evolution of Animal Behavior (BIO 245)
Ecological and evolutionary perspectives on animal behavior, with an emphasis on social and collective behavior. This is a project-based course in a lecture/seminar format. Seminars will be based on discussion of journal articles. Independent research projects on the behavior of animals on campus. Prerequisites: Biology or Human Biology core, Biology/ES 30. Recommended: statistics.
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.
Terms: Win
| Units: 4
| UG Reqs: GER: DB-NatSci
BIO 150:
Human Behavioral Biology (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.
Last offered: Spring 2016
| 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 152:
Imaging: Biological Light Microscopy (CSB 222, MCP 222)
Biological light microscopy: from theory to practice. This intensive laboratory and lecture course will provide participants with the theoretical and practical knowledge to utilize emerging imaging technologies. Students will learn the principles of light microscopy, as well as use of different types of cameras, laser scanning systems, functional fluorophores, probe delivery techniques. Topics include microscope optics, resolution limits, Koehler illumination, confocal fluorescence, two-photon, TIRF, FRET, photobleaching, super-resolution (SIM, STED, STORM/PALM), and live-cell imaging and cell tracking approaches. Discussion of physical principles; involves partial assembly and extensive use of lab instruments. Lab. Prerequisites: some college physics.
Terms: Spr
| 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.
Terms: Win
| 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, advanced biology course such as Bio104
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.
Last offered: Spring 2014
| 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.
Terms: Aut
| Units: 4
| UG Reqs: GER: DB-NatSci, WAY-SMA
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."
Last offered: Winter 2014
| Units: 1
BIO 167:
Insulin and carbohydrate metabolism in health and disease a history of advances 1850 to current
The quest to understand how the body uses sugar and the overlapping quest for a diabetes cure have resulted in discoveries in every branch of biology. Topics include insulin production, structure, and evolution; transduction of the insulin signal; transport of sugar into cells; sugar storage and release; how the brain transports and uses sugar; growth control; pancreas development; genetic and environmental causes of diabetes; engineering solutions to diabetes (artificial pancreas, stem cells), glucose homeostasis (modeling insulin action). Prerequisites: BIO 41, 42.
Terms: Spr
| Units: 3
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 and foster the development of strong scientific writing skills. We will review and discuss 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 present a current research paper in their preferred stem cell topic area and compose a novel research proposal. Prerequisites: Biology or Human Biology core. Satisfies WIM in Biology.
Terms: Aut
| Units: 3
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.
Terms: Aut
| Units: 3
| UG Reqs: GER: DB-NatSci
BIO 173:
Chemical Biology
Chemical biology is an integrative discipline that seeks to apply chemical tools and approaches to understand biology. This course will introduce students to various methods and approaches used in this field, with an emphasis on the use of natural products and synthetic small molecules as probes of biological function. Specific examples will be used to illustrate the ramifications of chemical biology with molecular, cell and developmental biology. The interaction between disease and drug discovery will be considered in detail. Prerequisites: Completion of BioCore (BIO 41, 42, 43).
Last offered: Spring 2016
| Units: 3
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 175:
Collective Behavior and Distributed Intelligence (SYMSYS 275)
This course will explore possibilities for student research projects based on presentations of faculty research. We will cover a broad range of topics within the general area of collective behavior, both natural and artificial. Students will build on faculty presentations to develop proposals for future projects.
Terms: Spr
| Units: 3
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 180:
Microbial Physiology (EARTHSYS 255, ESS 255, GS 233A)
Introduction to the physiology of microbes including cellular structure, transcription and translation, growth and metabolism, mechanisms for stress resistance and the formation of microbial communities. These topics will be covered in relation to the evolution of early life on Earth, ancient ecosystems, and the interpretation of the rock record. Recommended: introductory biology and chemistry.
Last offered: Autumn 2015
| 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: Win
| 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.
Last offered: Winter 2015
| 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, Spr
| 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);
Chen, X. (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);
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);
Mordecai, E. (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);
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);
Todhunter, A. (PI);
Tuljapurkar, S. (PI);
Vitousek, P. (PI);
Walbot, V. (PI);
Wang, Z. (PI);
Watt, W. (PI)
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 https://biology.stanford.edu/academics/undergraduate-research/directed-reading 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);
Chen, X. (PI);
Crowder, L. (PI);
Cyert, M. (PI);
Daily, G. (PI);
Denny, M. (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);
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);
Mordecai, E. (PI);
Morrison, A. (PI);
Mudgett, M. (PI);
Nelson, W. (PI);
Palumbi, S. (PI);
Petrov, D. (PI);
Pritchard, J. (PI);
Red-Horse, K. (PI);
Rosenberg, N. (PI);
Sapolsky, R. (PI);
Schnitzer, M. (PI);
Shatz, C. (PI);
Shen, K. (PI);
Sherlock, G. (PI);
Simon, M. (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)
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);
Chen, X. (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);
Klein, R. (PI);
Kopito, R. (PI);
Long, S. (PI);
Lowe, C. (PI);
Luo, L. (PI);
McConnell, S. (PI);
Micheli, F. (PI);
Mooney, H. (PI);
Mordecai, E. (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);
Tessier-Lavigne, M. (PI);
Thompson, S. (PI);
Tuljapurkar, S. (PI);
Vitousek, P. (PI);
Walbot, V. (PI);
Wang, Z. (PI);
Watt, W. (PI)
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 https://biology.stanford.edu/academics/undergraduate-research/research 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: ;
Artandi, S. (PI);
Attardi, L. (PI);
Barna, M. (PI);
Barres, B. (PI);
Beachy, P. (PI);
Bejerano, G. (PI);
Bergmann, D. (PI);
Bhatt, A. (PI);
Bhutani, N. (PI);
Block, B. (PI);
Block, S. (PI);
Brunet, A. (PI);
Butte, M. (PI);
Chang, H. (PI);
Cheng, A. (PI);
Chichilnisky, E. (PI);
Clandinin, T. (PI);
Clarke, M. (PI);
Crowder, L. (PI);
Cullen, M. (PI);
Cyert, M. (PI);
Daily, G. (PI);
Deisseroth, K. (PI);
Denny, M. (PI);
Diehn, M. (PI);
Dirzo, R. (PI);
Ehrlich, P. (PI);
Einav, S. (PI);
Feldman, M. (PI);
Felsher, D. (PI);
Fernald, R. (PI);
Field, C. (PI);
Fire, A. (PI);
Fordyce, P. (PI);
Francis, C. (PI);
Fraser, H. (PI);
Frydman, J. (PI);
Galli, S. (PI);
Giaccia, A. (PI);
Gilly, W. (PI);
Giocomo, L. (PI);
Gitler, A. (PI);
Gordon, D. (PI);
Gozani, O. (PI);
Graves, E. (PI);
Gross, E. (PI);
Gurtner, G. (PI);
Habtezion, A. (PI);
Hadly, E. (PI);
Hallmayer, J. (PI);
Hanawalt, P. (PI);
Heller, H. (PI);
Heller, S. (PI);
Hestrin, S. (PI);
Idoyaga, J. (PI);
Jarosz, D. (PI);
Jones, P. (PI);
Kao, P. (PI);
Khavari, P. (PI);
Kim, P. (PI);
Kim, S. (PI);
Knutson, B. (PI);
Kopito, R. (PI);
Kuo, C. (PI);
Levitt, M. (PI);
Li, G. (PI);
Li, J. (PI);
Lin, M. (PI);
Lipsick, J. (PI);
Long, S. (PI);
Longaker, M. (PI);
Lowe, C. (PI);
Luo, L. (PI);
MacIver, M. (PI);
Madison, D. (PI);
Majeti, R. (PI);
Martinez, O. (PI);
McConnell, S. (PI);
Micheli, F. (PI);
Mignot, E. (PI);
Monack, D. (PI);
Monje-Deisseroth, M. (PI);
Morrison, A. (PI);
Mudgett, M. (PI);
Nelson, W. (PI);
O'Brien, L. (PI);
O'hara, R. (PI);
Oghalai, J. (PI);
Oro, A. (PI);
Palmer, T. (PI);
Palumbi, S. (PI);
Pande, V. (PI);
Petrov, D. (PI);
Plant, G. (PI);
Porteus, M. (PI);
Prince, D. (PI);
Puglisi, J. (PI);
Quertermous, T. (PI);
Raymond, J. (PI);
Red-Horse, K. (PI);
Relman, D. (PI);
Ricci, A. (PI);
Rohatgi, R. (PI);
Sakamoto, K. (PI);
Sapolsky, R. (PI);
Schnitzer, M. (PI);
Shamloo, M. (PI);
Shatz, C. (PI);
Shen, K. (PI);
Shenoy, K. (PI);
Simon, M. (PI);
Skotheim, J. (PI);
Snyder, M. (PI);
Stearns, T. (PI);
Steinberg, G. (PI);
Stevenson, D. (PI);
Straight, A. (PI);
Sudhof, T. (PI);
Thompson, S. (PI);
Tuljapurkar, S. (PI);
Vitousek, P. (PI);
Walbot, V. (PI);
Wang, K. (PI);
Weis, W. (PI);
Weissman, I. (PI);
Wernig, M. (PI);
Wu, J. (PI);
Wu, S. (PI);
Wyss-Coray, T. (PI);
Yang, F. (PI);
Yang, Y. (PI);
Zhao, H. (PI);
Johnson, S. (GP)
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.
Last offered: Winter 2014
| Units: 3
BIO 204:
Neuroplasticity: From Synapses to Behavior
This course will focus on neuroplasticity from a broad perspective, from molecular cellular mechanism to its involvement in behavior and diseases. Emphasis will be on: a) molecular and cellular mechanisms underlying various forms of neuroplasticity; b) the neuroplasticity during brain development; c) the neuroplasticity in adult brain with respect to learning and memory; and d) maladaptive neuroplasticity in neurodegenerative disease and drug addiction. This course is designed for Ph.D. students from both the Biology and Neuroscience programs. Open to advanced undergraduates by consent of instructor.
Terms: Spr
| Units: 3
BIO 208:
Spanish in Science/Science in Spanish (EARTHSYS 207, LATINAM 207)
For graduate and undergraduate students interested in the natural sciences and the Spanish language. Students will acquire the ability to communicate in Spanish using scientific language and will enhance their ability to read scientific literature written in Spanish. Emphasis on the development of science in Spanish-speaking countries or regions. Course is conducted in Spanish and intended for students pursuing degrees in the sciences, particularly disciplines such as ecology, environmental science, sustainability, resource management, anthropology, and archeology.
Terms: Spr
| Units: 2
| Repeatable
2 times
(up to 4 units total)
BIO 210:
Chromatin Regulation of the Genome (BIO 110)
Maintenance of the genome is a prerequisite for life. In eukaryotes, all DNA-templated processes are tightly connected to chromatin structure and function. This course will explore epigenetic and chromatin regulation of cellular processes related to aging, cancer, stem cell pluripotency, metabolic homeostasis, and development. Course material integrates current literature with a foundational review of histone modifications and nucleosome composition in epigenetic inheritance, transcription, replication, cell division and DNA damage responses. Prerequisite: BIO 41 or consent of instructor.
Terms: Aut
| Units: 3
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, and differentiation. Weekly reading of current papers from the primary literature. Preparation of an original research proposal. Prerequisite for advanced undergraduates: BIO 129A,B, and consent of instructor.
Terms: Win
| Units: 4
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.
Last offered: Winter 2013
| 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. Enrollment is by application only. Recommended: background in neuroscience.
Terms: Spr
| Units: 3
BIO 223:
Stochastic and Nonlinear Dynamics (APPPHYS 223, BIOE 213)
Theoretical analysis of dynamical processes: dynamical systems, stochastic processes, and spatiotemporal dynamics. Motivations and applications from biology and physics. Emphasis is on methods including qualitative approaches, asymptotics, and multiple scale analysis. Prerequisites: ordinary and partial differential equations, complex analysis, and probability or statistical physics.
Terms: Spr
| Units: 3
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.
Last offered: Autumn 2015
| 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, microendoscopy, 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 238:
Ecosystem Services: Frontiers in 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. To apply, please email the instructor (gdaily@stanford.edu) with a brief description of your background and research interests.
Terms: Aut
| Units: 3
BIO 239:
The Hidden Kingdom - Evolution, Ecology and Diversity of Fungi (BIO 115)
Fungi are critical, yet often hidden, components of the biosphere. They regulate decomposition, are primary partners in plant symbiosis and strongly impact agriculture and economics. Students will explore the fascinating world of fungal biology, ecology and evolution via lecture, lab, field exercises and Saturday field trips that will provide traditional and molecular experiences in the collection, analysis and industrial use of diverse fungi. Students will chose an environmental niche, collect and identify resident fungi, and hypothesize about their community relationship. Prerequisite: Bio 43 recommended.
Last offered: Winter 2016
| Units: 4
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 245:
Ecology and Evolution of Animal Behavior (BIO 145)
Ecological and evolutionary perspectives on animal behavior, with an emphasis on social and collective behavior. This is a project-based course in a lecture/seminar format. Seminars will be based on discussion of journal articles. Independent research projects on the behavior of animals on campus. Prerequisites: Biology or Human Biology core, Biology/ES 30. Recommended: statistics.
Terms: Spr
| Units: 3
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.
Terms: Win
| 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.
Terms: Win
| Units: 3-5
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, advanced biology course such as Bio104
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.
Last offered: Spring 2014
| 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.
Terms: Aut
| Units: 4
BIO 263:
Neural Systems and Behavior (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.
Last offered: Autumn 2011
| Units: 4
BIO 267:
Molecular Mechanisms of Neurodegenerative Disease (GENE 267, 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 345)
Introduction to statistical and computational methods for genomics. Sample topics include: expectation maximization, hidden Markov model, Markov chain Monte Carlo, ensemble learning, probabilistic graphical models, kernel methods and other modern machine learning paradigms. Rationales and techniques illustrated with existing implementations used in population genetics, disease association, and functional regulatory genomics studies. Instruction includes lectures and discussion of readings from primary literature. Homework and projects require implementing some of the algorithms and using existing toolkits for analysis of genomic datasets.
Terms: Spr
| Units: 3
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.
Terms: Aut
| Units: 3
| UG Reqs: GER: DB-NatSci
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, ESS 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 and CEE 274B, 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: Win
| 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.
Last offered: Winter 2015
| Units: 3
BIO 286:
Natural History of the Vertebrates
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.
Last offered: Spring 2010
| 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.
Last offered: Spring 2016
| 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);
Chen, X. (PI);
Crowder, L. (PI);
Cyert, M. (PI);
Daily, G. (PI);
Denny, M. (PI);
Dirzo, R. (PI);
Dixon, S. (PI);
Ehrlich, P. (PI);
Endy, 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);
Goldbogen, J. (PI);
Gordon, D. (PI);
Gozani, O. (PI);
Greco, R. (PI);
Grossman, A. (PI);
Hadly, E. (PI);
Hanawalt, P. (PI);
Hekmat-Scafe, D. (PI);
Heller, H. (PI);
Heller, R. (PI);
Imam, J. (PI);
Jones, P. (PI);
Khalfan, W. (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);
Mordecai, E. (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);
Schwartz, E. (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);
King, D. (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: Sum
| Units: 1-3
BIO 294:
Cellular Biophysics (APPPHYS 294, BIOPHYS 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.
Last offered: Autumn 2015
| Units: 3
BIO 296:
TA Training in Biology
Workshop to provide teaching assistants in the Department of Biology with basic training, support, and professional development in their teaching roles. Should be taken concurrently with the first TA position.
Terms: Aut, Win, Spr
| Units: 1
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);
Mordecai, E. (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);
Rhee, S. (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)
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);
Axelrod, J. (PI);
Barna, M. (PI);
Barres, B. (PI);
Batzoglou, S. (PI);
Bergmann, D. (PI);
Bertozzi, C. (PI);
Bintu, L. (PI);
Blau, H. (PI);
Block, B. (PI);
Block, S. (PI);
Boothroyd, J. (PI);
Brandman, O. (PI);
Brown, P. (PI);
Brunet, A. (PI);
Brunger, A. (PI);
Bustamante, C. (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);
Demirci, U. (PI);
Denny, M. (PI);
Ding, J. (PI);
Dirzo, R. (PI);
Ehrlich, P. (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);
Freyberg, D. (PI);
Frommer, W. (PI);
Frydman, J. (PI);
Fukami, T. (PI);
Fuller, M. (PI);
Gardner, C. (PI);
Garner, C. (PI);
Gilly, W. (PI);
Gitler, A. (PI);
Glenn, J. (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);
Haskell, W. (PI);
Heilshorn, S. (PI);
Heller, H. (PI);
Heller, S. (PI);
Helms, J. (PI);
Herzenberg, L. (PI);
Hsu, S. (PI);
Jarosz, D. (PI);
Jones, P. (PI);
Katzenstein, D. (PI);
Kay, M. (PI);
Khavari, P. (PI);
Kim, S. (PI);
Koong, A. (PI);
Kopito, R. (PI);
Kornberg, A. (PI);
Krams, S. (PI);
Kuo, C. (PI);
Launer, A. (PI);
Lee, P. (PI);
Long, S. (PI);
Longaker, M. (PI);
Lowe, C. (PI);
Luo, L. (PI);
Lyons, D. (PI);
Maduke, M. (PI);
Marinkovich, M. (PI);
McConnell, S. (PI);
Micheli, F. (PI);
Mignot, E. (PI);
Miklos, D. (PI);
Mochly-Rosen, D. (PI);
Monack, D. (PI);
Montgomery, S. (PI);
Mordecai, E. (PI);
Morris, R. (PI);
Morrison, A. (PI);
Mudgett, M. (PI);
Murphy, G. (PI);
Nayak, N. (PI);
Nelson, W. (PI);
Nolan, G. (PI);
Nusse, R. (PI);
O'Brien, L. (PI);
O'hara, R. (PI);
Palumbi, S. (PI);
Parker, K. (PI);
Petrov, D. (PI);
Pollack, J. (PI);
Porteus, M. (PI);
Pringle, J. (PI);
Puglisi, J. (PI);
Rando, T. (PI);
Raymond, J. (PI);
Red-Horse, K. (PI);
Reimer, R. (PI);
Robinson, B. (PI);
Rosenberg, N. (PI);
Salzman, J. (PI);
Sapolsky, R. (PI);
Scherrer, G. (PI);
Schnitzer, M. (PI);
Scott, M. (PI);
Sebastiano, V. (PI);
Shapiro, L. (PI);
Shatz, C. (PI);
Shen, K. (PI);
Shenoy, K. (PI);
Sherlock, G. (PI);
Shooter, E. (PI);
Sibley, E. (PI);
Sikic, B. (PI);
Simon, M. (PI);
Skotheim, J. (PI);
Stearns, T. (PI);
Steinman, L. (PI);
Straight, A. (PI);
Theriot, J. (PI);
Thompson, S. (PI);
Tuljapurkar, S. (PI);
Vitousek, P. (PI);
Walbot, V. (PI);
Welander, P. (PI);
Wu, J. (PI);
Johnson, S. (GP);
Kanagawa, K. (GP);
Thompson, J. (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.
Last offered: Autumn 2015
| Units: 1
BIO 327:
Research Frontiers in Biodiversity and Ecosystem Services
This advanced seminar explores research frontiers in the science of biodiversity and ecosystem services. We will begin with foundational work and then shift to key frontiers now opening up ¿ including DNA barcoding, food web structure and ecosystem processes; remote sensing and modeling biodiversity change and ecosystem services; relating big data on natural capital and human well-being; and nature experience and human mental health. Students will lead discussions and make research presentations. To apply, please email the instructor (gdaily@stanford.edu).
Terms: Spr
| Units: 3
| Repeatable
2 times
(up to 6 units total)
BIO 328:
Managing Biodiversity Change: from Science to Policy
This course will explore key topics in management of biodiversity change at the science-policy interface. The topics will often be approached from an Iberian and Latin American perspective. Topics to be covered include: protected area management, ecological rewilding of abandoned farmland, agri-environmental schemes, developing biodiversity monitoring programs, developing biodiversity scenarios and identifying regional tipping points ecosystems; assessments across scales for the Intergovernmental Platform on Biodiversity and Ecosystem Services.
Terms: Win
| Units: 3
BIO 329:
Matrix Methods for Dynamic Models and Data Analysis
Types of matrices in dynamic & stochastic models, covariances, rectangular data, networks. Spectral theorem, asymptotics, stability theory, Nonnegative matrices, ergodicity, Markov chains. Hermitian, covariance, SVD. Perturbation theory. Random matrix products, Lyapunov exponents. Open to Ph.D. students in Biology. Prerequisites: Calculus (AP level) required. Some knowledge of linear algebra, R, preferred.
Terms: Aut
| Units: 1
BIO 330:
Stochastic Methods for Simulation, Dynamics and Data Analysis
Markov chains: ergodicity, CLT, passage times, absorption. Simulation: random numbers, chains. Poisson processes: applications and simulation. Time series models. MCMC essentials. Open to Ph.D. students in Biology. Prerequisites: Calculus (AP level) and basic linear algebra required. Facility with linear algebra, R, preferred.
Terms: Win
| Units: 1
BIO 331:
The Genetic Footprint of Latin America and its Impact in a Multicultural Society
This course will cover the latest advances in human population genomics with a particular focus on the evolutionary history of the Americas and the genetic population structure of Latin America. It is intended to suit a broad audience, including students in Biology, Genetics, Health Sciences, Anthropology, and Humanities. Therefore, topics will range from basic concepts in population genetics and DNA analysis techniques to specialized studies aimed at resolving fine-scale structure patterns in different regions across Latin America.
Terms: Spr
| Units: 3
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.
Last offered: Autumn 2014
| Units: 4
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: Win, Spr
| Units: 1-3
| Repeatable
for credit
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.
Terms: Win
| 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);
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);
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);
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);
Tuljapurkar, S. (PI);
Vitousek, P. (PI);
Walbot, V. (PI);
Wang, Z. (PI);
Watt, W. (PI);
Wong, W. (PI);
King, D. (GP)
