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. .
Last offered: Spring 2023
| Units: 3
| UG Reqs: WAY-SMA
BIO 3:
Frontiers in Ocean Science (OCEANS 3)
An introduction to contemporary research in ocean sciences, including oceanography, ecology, evolution, developmental biology, conservation, animal behavior, physiology, and sociological aspects. Emphasis is on new discoveries and the technologies used to make them. Weekly lectures and panel discussions by faculty from Oceans, Biology, and other departments.
Terms: Aut
| Units: 2
| Repeatable
2 times
(up to 4 units total)
BIO 4N:
The Science and Ethics of Personalized Genomic Medicine
We will explore the exciting field of personalized genomic medicine. Personalized medicine is based on the idea that each person's unique genome sequence can be used to predict their risk of developing diseases, and could perhaps even be edited using CRISPR to improve health. We will discuss the science behind these approaches; where they are heading in the future; and the ethical implications such technology presents. Student presentations will be emphasized, and students will also get to explore and analyze a real person's genome.
Terms: Win
| Units: 3
| UG Reqs: GER: DB-NatSci
BIO 5N:
Ants
Collective behavior, widespread in nature, operates without central control, using interactions among the participants. Ant colonies provide great opportunities to learn about collective behavior. Colonies consist of one or more reproductive females, which although they are called 'queens' do not direct the behavior of the rest of the colony, comprised of sterile female workers. Ants as a group are enormously diverse, with more than 14,000 species in every habitat on earth, and they show very diverse forms of collective behavior reflecting different ecological conditions. The course will include discussion of research about ant colony behavior, ecology, and evolution; a research project on campus involving observation and hypothesis testing; and, for the technologically-inclined, some simple simulations based on agent-based modeling.
Last offered: Winter 2023
| Units: 3
| UG Reqs: WAY-SMA
BIO 7N:
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. Cardinal Course certified by the Haas Center for Public Service.
Terms: Win
| Units: 3
| UG Reqs: WAY-CE
BIO 8N:
Human Origins
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.
Last offered: Winter 2023
| Units: 3
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 8S:
Introduction to Human Physiology
Normal functioning and pathophysiology of major organ systems: nervous, respiratory, cardiovascular, renal, digestive, and endocrine. Additional topics include integrative physiology, clinical case studies, and applications in genomics-based personalized medicine.
Terms: Sum
| Units: 4
| UG Reqs: GER: DB-NatSci
BIO 9N:
Chilis: Biology, History, Travels, Cuisine
Chili peppers are used worldwide. They are grown in astonishing variety even though they are used most often to flavor food. Yet the first chile peppers evolved in what Europeans call the New World (Central and South America). How do we know chilis came from the New World? How did they get to Europe, Africa, India, China? How did chilis become an integral part of so many cuisines? What forms of chili pepper do we find around the world?
Terms: Spr
| Units: 3
| UG Reqs: WAY-SMA
BIO 10N:
Using Physics to Explain Biology: Mechanistic Approaches to Plankton Ecology
People often think of physics and biology as entirely separate scientific pursuits, but in fact the two can be productively combined. All plants and animals live in a physical environment, and the laws of physics that govern that environment often determine how organisms function and interact. In this seminar, we will explore the confluence of physics and biology through an in-depth look at how phytoplankton and zooplankton -- the small algae and animals that form the base of the oceans' food web -- are affected by the physical properties of their watery world. You will be amazed by our ability to explain the ecology of these organisms, and how important that ecology is to life on earth.
Last offered: Autumn 2020
| Units: 3
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. 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.The 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. Students 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. 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.
Last offered: Summer 2023
| Units: 2
BIO 11S:
Microbiology: Human Health & Society
This course covers the fundamentals of microbiology and encompasses the tiny world of microbes (bacteria, archaea, fungi, viruses, and more). How have microbes impacted human health and society? It turns out that we cannot live without microbes, but we also have first-hand experience over the last few years of just how deadly and life-altering microbes can be! In exploring microbiology, we will take a multi-disciplinary approach combining molecular genetics (how gene expression is regulated in both prokaryotes and eukaryotes), biochemistry, and immunology. We will also explore key advances in biotechnology that have been made possible through our discovery of microbes and how they work including cloning, PCR, and CRISPR. This course will offer a laboratory component to allow students hands-on experience observing and working with bacteria and small eukaryotes and experimental design.
Terms: Sum
| Units: 5
| UG Reqs: WAY-SMA
BIO 12N:
Sensory Ecology of Marine Animals (OCEANS 12N)
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 15S:
Biology in the News
Biology is increasingly making its way into various aspects of our lives and will continue to do so throughout the 21st century. Thus, understanding the concepts underlying the headlines and their implications is very important and can help us engage meaningfully with the changing world around us. This course will begin by teaching skills like data interpretation and critical evaluation of logical arguments. With that foundation in place, we will then use specific, real-world events such as the FDA approval of GMO salmon, the development of the COVID-19 vaccines, and the fight against MRSA to explore the concepts in biology that underlie them (e.g. genetic modification, mRNA and vaccine development, and antibiotic resistance). Each week, students will be assigned to read news articles and informational materials giving background knowledge about the subject at hand. Each class will consist of a mini-lecture and in-class learning activities. The class will build towards a final project consisting of a podcast-style audio report on a biological process studied in the course. This course requires no prior background knowledge in biology and is intended for anyone interested in better understanding recent developments in the world of biology. By taking this course, students will learn basic concepts in biology and develop the skills necessary to critically evaluate arguments and the scientific data underlying those arguments.
Terms: Sum
| Units: 3
BIO 16:
Conservation Storytelling: Pre-course for BOSP South Africa
Limited to students admitted to the BOSP South Africa overseas seminar. Through 5 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 2020
| Units: 1
BIO 20S:
Climate Change Biology and Species Responses
This course offers a comprehensive examination of the ecological and biological consequences of climate change on diverse species and ecosystems. Students will explore the adaptive responses of animals, plants, and microbiomes to shifting environmental conditions. Additionally, the course will address the dynamic alterations in species ranges, changes in biotic interactions, and the implications of climate change on endangered species and environmental justice. Throughout the course, students will engage in group discussions centered on assigned scientific papers, honing their skills in critical thinking, interpretation, and presentation of findings. The course aims to equip students with a robust understanding of climate change biology while fostering teamwork and communication skills essential for tackling complex environmental challenges.
Terms: Sum
| Units: 3
BIO 25Q:
Cystic fibrosis: from medical conundrum to precision medicine success story
The class will explore cystic fibrosis (CF), the most prevalent fatal genetic disease in the US, as a scientific and medical whodunit. Through reading and discussion of medical and scientific literature, we will tackle questions that include: how was life expectancy with CF increased from weeks to decades without understanding the disease mechanism? Why is the disease so prevalent? Is there an advantage to being a carrier? Is CF a single disease or a continuum of physiological variation; or- what is a disease? How did research into CF lead to discovery of the underlying cause of most other genetic diseases as well? Through critical reading of the scientific and medical literature, class discussion, field trips and meetings with genetic counselors, caregivers, patients, physicians and researchers, we will work to build a deep understanding of this disease, from the biochemical basis to the current controversies over pathogenic mechanisms, treatment strategies and the ethics and economics of genetic testing and astronomical drug costs.
Terms: Win
| Units: 3
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 30:
Ecology for Everyone
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. The goal is to learn to think analytically about everyday ecological processes, including those that you participate in, which involve 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. The online version will meet synchronously and involve preparation outside of class for interactive discussions during class time. We will organize field projects that you can do wherever you are. Projects begin in the first week of the quarter. For questions please contact Prof. Gordon at dmgordon@stanford.edu.
Last offered: Winter 2021
| Units: 4
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 32S:
Introduction to Biotechnology: Detecting and Treating Disease
This course will examine the basic concepts of biotechnology and the instrumentation and techniques used in the manipulation of nucleic acids (DNA and RNA). Students will learn how biotechnology's tools and techniques are being used to help identify and fight disease, with a special emphasis on tools that help detect viral infections such as COVID-19. This course will also examine the ethical and privacy issues associated with biotechnology such as genetic testing, vaccine distributions, and gene therapy. Prerequisites: General biology and chemistry.Students are required to attend their assigned discussion section each week.
Terms: Sum
| Units: 3
BIO 35:
Sustainability and Civilization (HISTORY 35, POLISCI 35)
Our civilization faces multiple sustainability challenges. Climate change often dominates public conversation, but in fact, a whole range of environmental, economic, political, and cultural trends threaten the structures that sustain the societies we know. These problems cannot be understood in isolation, because they interact in complex ways. Solving them will require collaboration across many different fields, from the natural and social sciences to the humanities. This one-unit course brings together over two dozen faculty from across the entire university for a series of interdisciplinary conversations around cross-cutting themes. Our aim is to encourage dialogue and perhaps even future collaborations among students and professors who might otherwise rarely interact in a classroom. All students are welcome, but frosh and sophomores may find the course especially useful as an introduction to a wide range of sustainability-related disciplines and teachers at Stanford.
Terms: Win
| Units: 1
BIO 35N:
Catching up with Traditional Ecological Knowledge
Traditional ecological knowledge--the knowledge developed and maintained by local communities over many generations about their natural environment--is increasingly recognized as fundamental to solving environmental problems. In this seminar, we will explore some of the cutting-edge research on traditional ecological knowledge and its conceptual and practical role in ensuring environmental sustainability. We will address some key questions. For example, what makes traditional ecological knowledge different from Western science? What led to the recent increase in Western scientists' appreciation of traditional ecological knowledge? How can traditional ecological knowledge inform environmental sustainability in a world that is undergoing rapid climate change, land use change, and biological invasion? And how can Western science complement traditional ecological knowledge to achieve sustainability? The core of this seminar will be discussion based on reading of primary articles. We will also have field trips and learn from guest speakers.
Terms: Spr
| Units: 3
| UG Reqs: WAY-SMA
BIO 40S:
Advances in Cancer Biology Research and Cancer Treatments
Cancer is a ubiquitous global challenge - most families will be affected by it at some point in their lives. However, recent advancements in cancer treatment and prevention offer hope. In this course, we will delve into the fascinating world of cancer biology to explore groundbreaking research and treatment options. Diving deep into the inner workings of cancer cells, we will discover the potential of revolutionizing treatments such as CAR T immunotherapy, a cutting-edge technique that genetically modifies a patient's own immune cells to recognize and attack cancer cells. We'll also explore the crucial role of the cellular environment around tumors and learn how targeting this microenvironment can improve the effectiveness of existing therapies. We'll examine the unique nutrient requirements of cancer cells and how this knowledge can be used to selectively kill cancer cells while sparing healthy ones. And we'll discuss the power of biomarkers in developing tailored therapies that can significantly improve cancer patients' quality of life. Class sessions will include lectures and interactive discussions and activities. By the end of this course, students will have gained a solid understanding of cell biology, how cancer operates, and how - through scientific advances - it might eventually be stopped.
Terms: Sum
| Units: 3
BIO 43:
Introduction to Laboratory Research in Neuronal Cell Biology
This course provides an authentic research experience where you will study the consequences of disease-related mutations in a neuronal kinesin (KIF1A). You will evaluate scientific arguments; make discoveries by generating, testing, and revising hypotheses; communicate findings to others through oral and poster presentations; and build confidence in yourselves as scientific thinkers. To do so, you will use behavioral, genetic, and cell biological tools to assay how KIF1A mutations affect C. elegans neurons, and connect your findings to clinical severity. Completed or co-requisite in introductory courses in cell and molecular biology ( BIO 82 and 83 or HUMBIO 2A and 3A) and ( CHEM 31A and 31B or CHEM 31M).
Terms: Aut, Spr
| Units: 4
BIO 45:
Introduction to Laboratory Research in Cell and Molecular Biology
Use modern molecular approaches to characterize a particular tumor-associated mutation in the human p53 tumor suppressor gene via expression and analysis in a yeast model system. Learn about the role of p53 as Guardian of the Genome and consider novel p53-directed tumor therapies through lectures and by reading and discussing journal articles. Use molecular visualization programs to examine the structure of the normal p53 protein and localize the alteration induced by the mutation you are investigating. Assay the ability of mutant p53 to activate expression of multiple reporter genes. Through facilitated discussions with teams of other students studying the same p53 mutant, consider a series of molecular explanations for your p53 mutant's functional defects. Conduct lab experiments to test these hypotheses, analyze data, collaboratively interpret these data, and present your findings through a team oral presentation, as well as a scientific poster. Although there are no pre-requisites to enroll in this class, it will be helpful if you have already taken or are concurrently enrolled in introductory courses in cell and molecular biology (BIO 82 and 83 or HUMBIO 2A and 3A) and general chemistry (CHEM 31A and 31B or CHEM 31M).
Terms: Aut, Win
| Units: 4
Instructors: ;
Cyert, M. (PI);
Hekmat-Scafe, D. (PI);
Malladi, S. (PI);
Aizezi, Y. (TA);
Enam, U. (TA);
Hu, Y. (TA);
Nyame, K. (TA);
Pulido, E. (TA);
Rogers, A. (TA);
Sambel, L. (TA)
BIO 46:
Introduction to Research in Ecology and Evolutionary Biology (EARTHSYS 46)
The goal of this course is to develop an understanding of how to conduct biological research, using topics in Ecology as practical examples. This includes the complete scientific process: assessing background literature, generating testable hypotheses, learning techniques for data collection, analyzing data using appropriate statistical methods and writing and sharing results. 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 the statistical programming language R. The capstone of the course is a research paper in the style of a peer-reviewed journal article, as well as a group presentation designed for a general audience that communicates research findings. The Tuesday lecture session will generally meet for only about 60-70 minutes. IMPORTANT NOTE: Students who require BIO 46 to satisfy the WIM requirement for the Biology major MUST take this course for a letter grade. Please contact Elisa Mora (elisahm@stanford.edu) for logistical and enrollment questions.
Terms: Win
| Units: 4
| UG Reqs: WAY-SMA
BIO 47:
Introduction to Research in Ecology and Evolutionary Biology (EARTHSYS 47)
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 your 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 is an oral presentation of student teams' research findings, as well as a research paper written in the style of a peer-reviewed journal article. Labs will be completed both on campus and at Jasper Ridge. Although there are no pre-requisites to enroll in the class, it will be helpful if you have already taken BIO 81 or HUMBIO 2A. IMPORTANT NOTE: Satisfies WIM requirement in Biology but must be taken for a letter grade.
Terms: Spr
| Units: 4
BIO 50S:
Introduction to Cancer Biology
This course will examine the biological processes that are disrupted in cancer, such as DNA repair, cell cycle control, and signaling pathways. Students will learn the molecular mechanisms by which tumors gain and maintain a growth advantage and of potential therapeutic targets. This course will also explore the science behind cancer prevention, diagnosis, and treatments as well as emerging topics in the field such as cancer stem cells. Prerequisites: General biology & chemistry.Students are required to attend their assigned discussion section each week.
Terms: Sum
| Units: 3
| UG Reqs: WAY-SMA
BIO 52:
I, Scientist: Diversity Improves the Scientific Practice (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 scientific 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.
Last offered: Autumn 2018
| Units: 1
BIO 53:
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. Cardinal Course certified by the Haas Center for Public Service. This course is identical to Bio 7N, so students enrolled in the former should not take this course. Open to undergraduates and graduate students. Students must have access to a DSLR camera and lenses - we can accept up to 20 students who can share 10 course-provided cameras and lenses, by application. Application for camera use: https://forms.gle/1yAD3my8GoDseXw59.
Last offered: Winter 2023
| Units: 3
| UG Reqs: WAY-CE
BIO 63:
Science of Covid-19
This course is designed to help you solidify fundamental biology concepts and to appreciate their relevance to solving real world problems using Covid-19 as a case study. From the time we learned about the outbreak of a "pneumonia of unknown cause," we have learned so much. We will examine the origin of SARS-CoV-2, how it attacks cells, how the immune system responds, how viral variants emerge and how we can leverage all this information to design treatments and to address larger questions such as how this pandemic might end. Emphasis will be placed on critical thinking and scientific experimentation. You will use open-source online tools, read scientific papers on vaccine development and virus evolution, and use the skills you have developed to investigate a new area of research on Covid-19 that is of interest to you. This course is suitable for students who have taken a Foundations level course and/or AP biology, and have a basic understanding of DNA and how information in DNA is transcribed and translated to make proteins.
Last offered: Spring 2022
| Units: 4
| UG Reqs: WAY-SMA
BIO 71:
Planet Ocean (ESS 71, OCEANS 71)
Oceans make up the majority of our planet's area and living spaces and are fundamental to biodiversity, climate, food and commerce.This course covers integration of the oceanography and marine biology of diverse ocean habitats such as the deep sea, coral reefs, open ocean, temperate coasts, estuaries and polar seas. Lectures include state of the art knowledge as well as emerging technologies for future exploration. The second section focuses on how the oceans link to the global environment, and how ocean capacity helps determine human sustainability.
Terms: Win
| Units: 4
| UG Reqs: WAY-SMA
BIO 74:
Sustainability in Marine Organisms: Learning from the Evolutionary Survivors (OCEANS 74H)
While climate change has impacted life at land and sea, it's impossible to know exactly how fast species will adapt to warmer and more acidic sea water, and which species will survive into the future. In this course we will explore ancient marine organisms that have adapted and survived to diverse environmental changes across millions years of evolution, in order to better understand the molecular cellular and communal elements that allowed for their success. The course will include observation and experimentation with diverse marine organisms, lectures, readings, writings, and discussions. Course taught in-person only at Hopkins Marine Station. Round-trip university shuttle provided.
Terms: Win
| Units: 4
BIO 81:
Introduction to Ecology
This course will introduce you to the first principles of the science of ecology, the study of interactions between organisms and their environment. If you are on the waitlist, we will contact you during the first week of the quarter when we will have more information about your prospects for joining the course. Contact Lydia Villa (lydiav@stanford.edu) for logistical questions. Prerequisites: None.
Terms: Aut
| Units: 4
| UG Reqs: WAY-SMA
BIO 82:
Genetics
The focus of the course is on the basic mechanisms underlying the transmission of genetic information and on the use of genetic analysis to study biological and medical questions. Major topics will include: (1) the use of existing genetic variation in humans and other species to identify genes that play an important role in determining traits and disease-susceptibility, (2) the analysis of mutations in model organisms and their use in the investigation of biological processes and questions and (3) using genetic information for diagnosis and the potential for genetic manipulations to treat disease. Prerequisites: None, but BIO 83 is recommended. Lecture attendance as well as discussion section attendance is mandatory. Please only enroll in the lecture section (section 01) on Axess. Discussion section enrollment will be handled on Canvas. As long as you sign up for the lecture section on Axess, you will receive an e-mail a week before classes begin to guide you on how to sign up for a section on Canvas. For logistical questions about the course, please contact Waheeda Khalfan (wkhalfan@stanford.edu).
Terms: Win
| Units: 4
| UG Reqs: WAY-SMA
BIO 83:
Biochemistry & Molecular Biology
Introduction to the molecular and biochemical basis of life. Lecture topics include the structure and function of proteins, nucleic acids, lipids and carbohydrates, energy metabolism, signal transduction, epigenetics and DNA repair. The course will also consider how defects in these processes cause disease. Preliminary syllabus will be posted by Sep 1st on Stanford Syllabus. If you are on the waitlist, we will contact you during the first week of the quarter when we will have more information about your prospects for joining the course. Contact Waheeda Khalfan (wkhalfan@stanford.edu) for logistical questions. Prerequisites: None.Please only enroll in the lecture section (section 01) on Axess. Discussion section enrollment will be handled on Canvas. As long as you sign up for the lecture section on Axess, you will receive an e-mail a week before classes begin to guide you on how to sign up for a section on Canvas.
Terms: Aut
| Units: 4
| UG Reqs: WAY-SMA
BIO 84:
Physiology
The focus of Physiology is on understanding how organisms tackle the physical challenges of life on Earth. This course will provide an overview of animal and plant physiology and teach an understanding of how organisms maintain homeostasis, respond to environmental cues and coordinate behaviors across multiples tissues and organ systems. We will examine the structure and function of organs and organ systems and how those systems are controlled and regulated to maintain homeostasis. Control and regulation requires information as does the ability to respond to environmental stimuli, so we will give special consideration to hormonal and neural information systems. We will also be concerned with the interactions and integration of the activities of the different organ systems we study. Prerequisites: none. The course will have in person exams. Lecture attendance as well as discussion section attendance is mandatory. Please only enroll in the lecture section (section 01) on Axess. Discussion section enrollment will be handled on Canvas. As long as you sign up for the lecture section on Axess, you will receive an e-mail a week before classes begin to guide you on how to sign up for a section on Canvas. For logistical questions about the course, please contact Waheeda Khalfan at wkhalfan@stanford.edu.
Terms: Win
| Units: 4
| UG Reqs: WAY-SMA
BIO 85:
Evolution
Understanding evolution is key to understanding the diversity of life on earth. We will be focusing on the fundamental principles of evolutionary biology from natural and sexual selection to the formation of new species. To understand these concepts we will delve into the mechanisms that underlie them. The course will also link these fundamental processes to important contemporary evolutionary topics such as the evolution of behavior, life history evolution, and human evolution. Prerequisites: BIO 60 or 61 or 62 or equivalent; recommended: BIO 82, or permission of instructor.
Terms: Win
| Units: 4
| UG Reqs: WAY-SMA
BIO 86:
Cell Biology
This course will focus on the basic structures inside cells and how they execute cellular functions. Topics include organelles, membrane trafficking, the cytoskeleton, cell division, and signal transduction. Classic and recent primary literature will be incorporated into lectures with an emphasis on state of the art experimental approaches. Prerequisites: BIO 83 is highly recommended.
Terms: Spr
| Units: 4
| UG Reqs: WAY-SMA
BIO 101:
Science for Conservation Policy: Meeting California's Pledge to Protect 30% by 2030 (EARTHSYS 101C)
California has set the ambitious goal of conserving 30% of its lands and waters by the year 2030. In this course, students will develop science-based recommendations to help policymakers reach this '30 by 30' goal. Through lectures, labs, and field trips, students will gain practical skills in ecology, protected area design in the face of climate change, and science communication. Students will apply these skills to analyze real-world data, formulate conservation recommendations, and communicate their findings in verbal and written testimony to policymakers. Prerequisites: BIO 81 or BIO/EARTHSYS 105 or BIO/EARTHSYS 111 or instructor approval.
Terms: Win
| Units: 4
| UG Reqs: WAY-AQR
BIO 102:
Introduction to Neuroscience
This course introduces key concepts and exciting research in neuroscience to students interested in how the brain enables us to sense, act, think, and remember. The course spans all levels of inquiry, from molecules to cells, circuits, systems, and animal behavior. The process of discovery will be emphasized, and students will interact in class with scientists who made key discoveries. Lectures follow the textbook "Principles of Neurobiology" written by the instructor. No prerequisites other than a keen curiosity about the brain.
| Units: 4
BIO 105:
Microbes and Climate (BIO 205, ESS 122, ESS 222)
Microorganisms drive the cycling of carbon, oxygen, and other nutrients in the earth system. This means that microbes both impact and are impacted by changes in climate. In this reading course, participants will read and present a combination of classic and current papers in the primary literature. Topics will include: the co-evolution of microbial metabolism and the climate system over geological timescales; impacts of current climate change on microbial physiology, community ecology, and ecosystem function; multiple stressors; feedbacks of microbial communities to anthropogenic greenhouse gas emissions; methods for connecting microbial activities to climate dynamics in process models.
Last offered: Autumn 2022
| Units: 1
BIO 105A:
Ecology and Natural History of Jasper Ridge Biological Preserve (EARTHSYS 105A)
The Ecology and Natural History of the Jasper Ridge Biological Preserve is an upper-division course that aims to help students learn ecology and natural history using a 'living laboratory,' the Jasper Ridge Biological Preserve. The course's central goal is that, as a community of learning, we examine 'via introductory discussions, followed by hands-on experiences in the field' the scientific basis of ecological research, archaeology, edaphology, geology, species interactions, land management, and multidisciplinary environmental education. The first 10 sessions that compose the academic program are led by the instructors, faculty (world-experts on the themes of each session), and JRBP staff. In addition, this 20-week class (winter and spring quarters) trains students to become JRBP Docents that will join the Jasper Ridge education affiliates community. Completion of both Winter (BIO 105A) and Spring (BIO 105B) sequence training program is required to join the Ecology and Natural History of Jasper Ridge Biological Preserve course.
Terms: Win
| Units: 4
BIO 105B:
Ecology and Natural History of Jasper Ridge Biological Preserve (EARTHSYS 105B)
The Ecology and Natural History of the Jasper Ridge Biological Preserve is an upper-division course that aims to help students learn ecology and natural history using a 'living laboratory,' the Jasper Ridge Biological Preserve. The course's central goal is that, as a community of learning, we examine 'via introductory discussions, followed by hands-on experiences in the field' the scientific basis of ecological research, archaeology, edaphology, geology, species interactions, land management, and multidisciplinary environmental education. The first 10 sessions that compose the academic program are led by the instructors, faculty (world-experts on the themes of each session), and JRBP staff. In addition, this 20-week class (winter and spring quarters) trains students to become JRBP Docents that will join the Jasper Ridge education affiliates community. Completion of both Winter (BIO 105A) and Spring (BIO 105B) sequence training program is required to join the Ecology and Natural History of Jasper Ridge Biological Preserve course.
Terms: Spr
| Units: 4
BIO 109A:
Chronic Disease I: Applications of Novel Advances in Biology and Biotechnology
We have come a long way in developing therapies for chronic diseases. However, a gap remains between the current solutions and our ability to fully address these diseases. This course provides an overview of: (1) the underlying biology of many of these diseases and (2) the applications of novel advances in basic science and biotechnology to generate more effective therapies. There will be guest lectures from prominent leaders in academia and industry, and we encourage both students and speakers to seek opportunities to collaborate. No hard prerequisites, though a basic understanding of biology and willingness to learn novel concepts will help.
Last offered: Winter 2023
| Units: 3
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 109B:
Chronic Disease II: Applications of Advances in Precision Medicine and Digital Health Technologies
Chronic diseases fatally impact over 40 million people worldwide. We have come a long way in developing therapies for some chronic diseases, but a considerable gap remains between the current solutions and our ability to fully address many of these diseases. This course provides an overview of: (1) the underlying biology of pervasive chronic diseases and (2) the applications of advances in precision medicine and digital health technologies towards better understanding, preventing, and treating these diseases. There will also be discussions on the policy and regulatory frameworks and business and ethical implications that impact precision medicine/digital health innovations (and their potential applications). We will have guest speakers who are prominent leaders in academia, industry, and federal policy. We encourage both students and speakers to seek opportunities to collaborate. No hard prerequisites, though a basic understanding of biology and willingness to learn novel concepts will help.
Last offered: Spring 2023
| Units: 3
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 110:
The Chromatin-Regulated 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 BIO 83 or consent of instructor.
Last offered: Spring 2022
| Units: 3
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 111:
Microbiology
Introduction to microbiology, with emphasis on bacteria. Topics include the cell structure of microorganisms, gene regulation, bacterial genetics, bacterial evolution and diversity, bacterial development, interaction and communication, bacterial chemotaxis and motility, microbiomes, infectious diseases, bacterial pathogenesis, host defense systems, and viruses. Strongly recommended: molecular biology, biochemistry, genetics or cell biology courses (e.g. BIO 82, 83 or 86).
Terms: Win
| Units: 3
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: HUMBIO3A or HUMBIO4A or BIO83 or BIO84 orBIO86 or consent of instructor.
Terms: Win
| Units: 4
| UG Reqs: GER: DB-NatSci, WAY-SMA
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. Prerequisites: Biology core or BIO 82, 85 or graduate standing in any department, and consent of instructor.
Terms: Win
| Units: 4
| UG Reqs: GER: DB-NatSci
BIO 114A:
bioBUDS: Building Up Developing Scientists
BUDS is a student-centered and community-focused program which aims to connect all undergrads - but especially those from FLI and historically excluded backgrounds - to resources, skills, and potential mentors in the biosciences and beyond while fostering a vibrant peer community. We offer weekly grad student-led workshops covering a broad range of biological topics and special topic sessions (workshops, panels, community discussions). The Fall quarter session emphasizes growth as a scientist, seeking opportunities, and getting started in research. All sessions are open to all students regardless of course enrollment, department affiliation, experience-level, or field. For more information, visit our website: https://biobuds.stanford.edu.
Terms: Aut
| Units: 2
BIO 114B:
bioBUDS: Building Up Developing Scientists
BUDS is a student-centered and community-focused program that aims to connect all undergrads - but especially those from FLI and historically excluded backgrounds - to resources, skills, and potential mentors in the biosciences and beyond while fostering a vibrant peer community. We offer weekly grad student-led workshops covering a broad range of biological topics and special topic sessions (workshops, panels, community discussions). The Winter quarter session emphasizes biology at the intersection of other sciences and humanities. All sessions are open to all students regardless of course enrollment, department affiliation, experience level, or field. Visit our website here: https://biobuds.stanford.edu.
Terms: Win
| Units: 2
BIO 114C:
bioBUDS: Research Program
This course serves as a companion and continuation for the Fall and Winter sessions of bioBUDS ( BIO 114A and 114B). If demand exceeds slots available, preference will be given to students who participated in the Fall and/or Winter sessions. This program will pair participating students with a lab/research mentor based on student-ranked preferences. Students will work on a research project with their mentor for the duration of the quarter. Enrollment in BIO114C is required to participate in the internship, and class sessions will focus on tracking internship progress and evaluating mentorship relationships. For information, visit our website: https://biobuds.stanford.edu. An application link will be available on our website in early February.
Terms: Spr
| Units: 2
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 81, 85 recommended.
Terms: Win
| Units: 4
| UG Reqs: WAY-SMA
BIO 116:
Ecology of the Hawaiian Islands (SUSTAIN 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 Wrigley Field Program in Hawaii.
Last offered: Autumn 2022
| Units: 4
| UG Reqs: GER: DB-NatSci
BIO 117:
Biology and Global Change (EARTHSYS 111, EARTHSYS 217, 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 BIO 81 or graduate standing.
Terms: Win
| Units: 4
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 120:
Integrative and Experimental Microbiology (BIO 220)
To survive, grow, and reproduce, organisms coordinate different molecular processes so they can use available resources and cope with environmental conditions. This laboratory course explores molecular and cellular integration in bacteria. Experiments include the quantification of growth, mutational screens and mutant analysis, gene cloning, and measuring/engineering gene-expression. These "wet lab" approaches will be combined with "dry lab" approaches to analyze experimental findings and explore further the link between molecular processes, cell-physiology, and ecology. Prerequisite: MATH 51 or MATH 19, 20,21. Recommended: microbiology (e.g. BIO 62 or 162) and molecular biology/biochemistry/genetics courses (e.g. BIO 82 or 83). Enrollment via Application: https://forms.gle/etRHRhhaRJxUMyNW9
Terms: Spr
| Units: 3
| Repeatable
1 times
(up to 3 units total)
BIO 121:
Ornithology (BIO 221)
Advanced undergraduate survey of ornithology, introducing students to the biology of birds and giving them to tools to use birds as model systems for research. Topics will include avian evolution, physiology, adaptations, behavior, and ecology. Focus throughout on identification of California birds and applications to current bird conservation issues. Course will include lectures and a field component which will expose students to standard avian research techniques such as mistnetting, banding, and point count surveys. Prerequisite: BIO 81 or BIO 105A/B or instructor approval.
Terms: Spr
| Units: 3
BIO 123:
Catalyzing Solutions for a Sustainable Ocean: Learning with Local Communities (OCEANS 123H, OCEANS 223H)
The ocean is impacted by overfishing, plastic pollution, climate change and acidification, which are leading to the disruption of marine ecosystem functions and services critical for human wellbeing. Ocean mining, offshore wind farming, increasing shipping, land sea interactions and carbon sequestration are all posing a whole new set of unprecedented challenges and, at the same time, opportunities to solve the pressing problem humanity has to face. By leveraging the unique location of Hopkins Marine Station as a living laboratory in Monterey Bay, this course will provide a unique opportunity for students to learn through real world examples about the multifaceted nature of problems at the very core of ocean sustainability. Course taught in-person only at Hopkins Marine Station; for information on how to spend spring quarter in residence: https://hopkinsmarinestation.stanford.edu/undergraduate-studies/spring-courses-23-24 (Individual course registration also permitted.) Depending on enrollment numbers, a weekly shuttle to Hopkins or mileage reimbursements for qualifying carpools will be provided; terms and conditions apply.
Terms: Spr
| Units: 3
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: Human Biology core or BIO 82, 83, 86, or with permission of instructor.
Terms: Aut
| 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 127:
Genomic approaches to the study of human disease (BIO 247, GENE 247)
This course will cover a range of genetic and genomic approaches to studying human phenotypic variation and disease. We will discuss the genetic basis of Mendelian and complex diseases, as well as clinical applications including prenatal testing, and pediatric and cancer diagnostics. The course will include lectures as well as critical reading and discussion of the primary literature. Prerequisite: BIO 82 or equivalent. Open to advanced undergraduate students.
Terms: Win
| Units: 3
BIO 129:
Fundamentals and Frontiers in Plant Biology (BIO 229)
This course will serve as a primer for all levels of graduate, co-term, and upper-level undergraduates interested in learning about the fundamental aspects of plant biology, the latest advances in tools, techniques, and theories that link basic science with translational science and applications for solving major societal challenges of today and tomorrow. In addition, this course will serve to introduce the breadth of plant research on campus and help solidify a cohort of students interested in plant biology.
Last offered: Spring 2022
| Units: 3
| Repeatable
2 times
(up to 6 units total)
BIO 130:
Ecosystems of California (EARTHSYS 130A)
California is home to a huge diversity of ecosystem types and processes. This course provides an introduction to the natural history, systematics, and ecosystem ecology of California ecosystems, based on a combination of lectures, student-led projects, and weekend field trips. Ecosystems to be explored will range from coasts to mountains and from desert to wetlands. Requirements include three essays and participation in three field trips (of six options).
Last offered: Spring 2019
| Units: 4
BIO 132:
Advanced Imaging Lab in Biophysics (APPPHYS 232, BIO 232, BIOE 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, basic cell biology, and consent of instructor.
Terms: Spr
| Units: 4
| UG Reqs: GER: DB-NatSci
BIO 134:
Molecular and cellular analysis of human cancer cell lines
This laboratory course will use cultured mammalian cells to study whether drug treatment can restore function to mutant versions of the tumor suppressor p53. Students will perform a variety of cellular and molecular techniques, including western blot and immunofluorescence, to test certain abilities of their mutant in the presence and absence of the drug. The project will culminate with student-designed experiments testing a functional aspect of p53 and presentation of the results for both expert and lay audiences. Strongly suggested prerequisites: BIO 45, BIO 82, 83, 86. Enrollment very limited; application required. Apply by 2/10/23 at: https://docs.google.com/forms/d/e/1FAIpQLSeIZAf2oAqwu8y9RMca4BjPTo8coCHl2asCk24kHMvGxPNlfg/viewform?usp=sf_link
Last offered: Spring 2023
| Units: 5
BIO 136:
Macroevolution (BIO 236, EPS 136, EPS 236)
(Formerly GEOLSCI 136 and 236) The course will focus on the macroevolution of animals. We will be exploring how paleobiology and developmental biology/genomics have contributed to our understanding of the origins of animals, and how patterns of evolution and extinction have shaped the diversity of animal forms we observe today. Change of Department Name: Earth and Planetary Science (Formerly Geologic Sciences).
Terms: Spr
| Units: 3
| UG Reqs: WAY-SMA
BIO 139:
Pattern Formation
We have all seen patterns in nature: from zebra stripes to spiraling flower petals to ordered rows of microscopic appendages on single celled pond organisms. But how are these patterns generated, what are they good for, and are patterns in different species related? This upper level course in cell and developmental biology will explore how patterns emerge in cells and organisms and through evolution, touching on topics in cell polarity and adhesion, cell differentiation, cell-cell signaling, morphogenesis, and growth control. BIO 83, BIO 86 or equivalent; BIO160 or BIO158 recommended.
Last offered: Winter 2022
| Units: 3
BIO 140:
The Science of Extreme Life of the Sea (OCEANS 141H)
Covers the way marine animals and plants live in extreme environments by examining morphological, ecological, and genetic adaptations to low temperature, high heat, deep water, etc. We also cover extreme lifestyles such as fast swimming, small and large body size, and novel reproductive systems. Lecture material is punctuated with a series of tutorials on narrative writing skills in science, especially creative non-fiction, memoirs, braided essays and short fiction. The goal is to integrate quantitative thinking about the life sciences with creative writing that brings facts to life. Prerequisites: core courses in biology, creative writing, environmental sciences or engineering. Course taught in-person only at Hopkins Marine Station. For information about how to spend spring quarter in residence in Monterey: https://hopkinsmarinestation.stanford.edu/undergraduate-studies/spring-courses-23-24. Individual course registration also permitted; no application required. Depending on enrollment numbers, a weekly shuttle to Hopkins or mileage reimbursements for qualifying carpools will be provided; terms and conditions apply.
Last offered: Spring 2022
| Units: 3
| UG Reqs: WAY-CE
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: Win
| Units: 5
| UG Reqs: GER:DB-Math, WAY-AQR
BIO 142:
Molecular Geomicrobiology Laboratory (EARTHSYS 143, ESS 143, ESS 243)
In this course, students will be studying the biosynthesis of cyclic lipid biomarkers, molecules that are produced by modern microbes that can be preserved in rocks that are over a billion years old and which geologist use as molecular fossils. Students will be tasked with identifying potential biomarker lipid synthesis genes in environmental genomic databases, expressing those genes in a model bacterial expression system in the lab, and then analyzing the lipid products that are produced. The overall goal is for students to experience the scientific research process including generating hypotheses, testing these hypotheses in laboratory experiments, and communicating their results through a publication style paper. Prerequisites: BIO83 and CHEM 121 or permission of the instructor.
Last offered: Spring 2022
| Units: 3-4
| UG Reqs: WAY-SMA
BIO 143:
Quantitative Methods for Marine Ecology and Conservation (BIO 243, CEE 164, CEE 264H, EARTHSYS 143H, EARTHSYS 243H, OCEANS 143)
NOTE: This course will be taught in-person on main campus, in hybrid format with Zoom options. The goal of this course is to learn the foundations of ecological modeling with a specific (but not exclusive) focus on marine conservation and sustainable exploitation of renewable resources. Students will be introduced to a range of methods - from basic to advanced - to characterize population structure, conduct demographic analyses, estimate extinction risk, identify temporal trends and spatial patterns, quantify the effect of environmental determinants and anthropogenic pressures on the dynamics of marine populations, describe the potential for adaptation to climate change. This course will emphasize learning by doing, and will rely heavily on practical computer laboratories, in R and/or Phyton, based on data from our own research activities or peer reviewed publications. Students with a background knowledge of statistics, programming and calculus will be most welcome. Formally BIOHOPK 143H and 243H.
Terms: Win
| Units: 4
| UG Reqs: WAY-AQR, WAY-FR
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 the 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. All students will be expected to conduct a literature research exercise leading to a written report, 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:
Animal Behavior (BIO 245)
Animal behavior with an emphasis on social and collective behavior. How do animals interact with each other and the rest of the world around them? This is a project-based course in a seminar format, including class discussion of journal articles, and independent research projects based on observing the behavior of animals on campus. Prerequisites suggested: Biology or Human Biology core or BIO 81 and 85 or consent of instructor; BIO/ES 30. Recommended: some background in statistics.
Terms: Win
| Units: 3
| UG Reqs: GER: DB-NatSci
BIO 146:
Genes and Disease
Students in this course will uncover key principles of genetics and molecular biology through investigation of case studies of human disease and novel therapeutic approaches in development. This course will require close reading and discussion of primary literature and will emphasize and support the development of critical skills in scientific communication. Students will utilize a variety of mediums to convey scientific information to a range of audiences in a series of projects completed during the quarter. Prerequisites: BIO 82, 83 and 86 or equivalent.
Terms: Spr
| Units: 3
BIO 147:
Ecosystem Ecology and Biogeochemistry (BIO 240, EARTHSYS 147, EARTHSYS 247)
An introduction to ecosystem ecology and terrestrial biogeochemistry. This course will focus on the dynamics of carbon and other biologically essential elements in the Earth System, on spatial scales from local to global. Prerequisites: Biology 117, Earth Systems 111, or graduate standing.
Last offered: Autumn 2021
| Units: 3
BIO 148:
Evolution of Terrestrial Ecosystems (BIO 228, EARTHSYS 128, EPS 128, EPS 228)
(Formerly GEOLSCI 128 and 228) The what, when, where, and how do we know it regarding life on land through time. Fossil plants, fungi, invertebrates, and vertebrates (yes, dinosaurs) are all covered, including how all of those components interact with each other and with changing climates, continental drift, atmospheric composition, and environmental perturbations like glaciation and mass extinction. The course involves both lecture and lab components. Graduate students registering at the 200-level are expected to write a term paper, but can opt out of some labs where appropriate. Change of Department Name: Earth and Planetary Science (Formerly Geologic Sciences).
Last offered: Winter 2023
| Units: 4
| UG Reqs: WAY-SMA
BIO 149:
The Neurobiology of Sleep (BIO 249, HUMBIO 161, PSYC 149, PSYC 261)
The neurochemistry and neurophysiology of changes in brain activity and conscious awareness are associated with changes in the sleep/wake state. Behavioral and neurobiological phenomena include sleep regulation, sleep homeostasis, circadian rhythms, sleep disorders, sleep function, and the molecular biology of sleep. Preference to seniors and graduate students.
Terms: Win
| Units: 4
| UG Reqs: GER: DB-NatSci, WAY-SMA
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.
Terms: Spr
| Units: 5
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 151:
Mechanisms of Neuron Death
For undergraduates with backgrounds 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. Assessment based on in-class participation and short weekly papers. Enrollment is limited to 15; an application is required. Enrollment by permission of professor, apply at https://forms.gle/bb9bXf1wGHFiuTAn8
Terms: Aut
| Units: 3
| UG Reqs: GER: DB-NatSci
BIO 152:
Imaging: Biological Light Microscopy (MCP 222)
This intensive laboratory and discussion course will provide participants with the theoretical and practical knowledge to utilize emerging imaging technologies based on light microscopy. Topics include microscope optics, resolution limits, Köhler illumination, confocal fluorescence, two-photon, TIRF, FRET, photobleaching, super-resolution (SIM, STED, STORM/PALM), tissue clearing/CLARITY/light-sheet microscopy, and live-cell imaging. Applications include using fluorescent probes to analyze subcellular localization and live cell-translocation dynamics. We will be using a flipped classroom for the course in that students will watch iBiology lectures before class, and class time will be used for engaging in extensive discussion. Lab portion involves extensive in-class use of microscopes in the CSIF and NMS core microscopy facilities.
Terms: Aut
| Units: 3
| UG Reqs: GER: DB-NatSci
BIO 154:
Principles of Neurobiology
For advanced undergraduate students. Principles and mechanisms in the organization and functions of the nervous system. Topics: neuronal communication, sensory and motor systems, innate behaviors, learning and memory, brain disorders, and evolution of the nervous system.
Last offered: Winter 2023
| Units: 4
| UG Reqs: GER: DB-NatSci
BIO 155:
Cell and Developmental Biology of Plants (BIO 255)
In this course we will learn how plants are built at different organizational scales from the cell, tissue, organ and organ system level. We will also learn about the experimental methods used to study plants at these different organizational levels and how to interpret and evaluate experiments that use such methods. Finally, advances in genetic engineering will be discussed as a means of manipulating the form and function of plants for sustainable agriculture. Broadly relevant skills that will be cultivated in the course include: evaluating primarily literature, identifying gaps in knowledge, formulating research questions and designing new experimental strategies. Prerequisites: BIO 80 series or equivalent.
Last offered: Autumn 2022
| Units: 3
| UG Reqs: WAY-SMA
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. Prerequisites: BIO 82, 83, 84, 86.
Last offered: Autumn 2022
| Units: 4
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 159:
Herpetology
This course introduces students to herpetology or the study of reptiles and amphibians. Students will learn foundational concepts in reptile and amphibian evolution, physiology, behavior, and ecology through hands-on experiences. This course includes two field-based modules: one centering on local salamander populations and the other a general survey of the amphibian and reptile biodiversity on campus. Additionally, a student-driven and designed laboratory experiment will allow students to apply and connect course concepts about behavior and physiology. Students will learn to analyze, visualize and present data from field and laboratory experiments. Student involvement in local monitoring efforts will contribute to the ongoing conservation of amphibians and reptiles on campus. Prerequisites: BIO 30 (Ecology for Everyone) or BIO 81 (Ecology) or BIO 84 (Physiology) required or concurrent.
Last offered: Winter 2023
| Units: 3
BIO 160:
Developmental Biology
This course will cover the molecular mechanisms underlying the generation of diverse cell types and tissues during embryonic and post-embryonic animal development. Topics include the role of cell-cell communication in controlling developmental decisions, the organization and patterning of large groups of cells via morphogen signaling, the specification of individual cell types, and the role of stem cells in development. The course emphasizes the experimental logic and methods of research in developmental biology and includes discussions of research papers.
Terms: Win
| Units: 4
BIO 161:
Organismal Biology Lab
This laboratory is a genuine research experience course where students contribute to original research in a field of organismal biology. The course consists of two modules: In the first module, students will perform a drug screen for novel compounds that influence animal behavior by altering nervous system function. In the second module, students will explore how the microbiome of animals is important for health and social interactions. Students work collaboratively to collect and analyze data and communicate their findings through oral and written formats.
Terms: Aut
| Units: 4
| UG Reqs: WAY-SMA
BIO 162:
Mechanisms of Tissue Regeneration
Many organisms possess a remarkable ability to repair and regenerate damaged organs and tissues. This course will explore the cellular and developmental mechanisms used to achieve regeneration. Students will learn the basic developmental and cellular mechanisms underlying the original formation of organs during normal development and how these mechanisms are modified during the regenerative process. The course will also consider how our expanding knowledge of regeneration mechanisms could be used to promote medically useful regeneration in humans. The course will involve extensive reading and analysis of primary literature. Prerequisites: BIO 86 (BIO 160 or BIO 158 recommended). Enrollment by permission of professor, apply at https://forms.gle/uoGrzagSRdTGd2hU8.
Terms: Spr
| Units: 3
BIO 164:
Plant Ecology & Evolution in Arid Climates (BIO 224, EARTHSYS 224)
Understanding responses of plants to climate change is paramount to protect our ecosystems. In this course, we will review classical work on fundamental concepts of plant biology and evolutionary ecology in arid climates. We will study plant biodiversity patterns in arid climates, we will collect and investigate plants and their ecophysiological stress coping strategies, and we will learn how to use genomics to understand plant adaptation. The course will introduce some new technologies, such as bioinformatic tools, DNA sequencing, biodiversity databases, etc. And we will have field trips to Jasper Ridge and other ecosystems to see living examples across the California landscape. Enrollment limited; application required. Apply at https://docs.google.com/forms/d/e/1FAIpQLScWPTN4HI-IUoFhgOMaXwFVpGZnOB5-9O0qufaObYf5iAK6KA/viewform.
Last offered: Spring 2023
| Units: 3
BIO 165:
Quantitative Approaches in Modern Biology (BIO 265)
Modern research approaches tightly integrate experimentation with data analysis and mathematical modeling to provide unprecedented insights into the organization and functioning of living systems. This course explores the quantitative basis of major cellular processes and their coordination to form a cohesive physiological entity that is capable of rapid growth and acclimation to changing environments. Weekly lectures will be accompanied by 'dry lab sessions' in which students analyze experimental data sets and discuss the challenges of accomplishing rigorous and reproducible research. As such, students will actively develop a fundamental skill set of quantitative biology which includes knowledge in coding, dynamical systems modeling, and statistics. Assumes basic (but not advanced) familiarity with math, e.g. MATH51. Enrollment by permission of the professor, apply at https://forms.gle/j6ocJs8fQFPK1GGLA.
Terms: Win
| 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 or BIO 82, 83, 86. Satisfies WIM in Biology.
Last offered: Autumn 2022
| Units: 3
BIO 169:
The Sixth Extinction (and the Other Five) (BIO 237, EARTHSYS 127A, EARTHSYS 227A, EPS 137, EPS 237)
(Formerly GEOLSCI 137 and 237) Are we living through Earth's sixth major mass extinction event? The course will address the causes and consequences of extinction. It will review current understanding of background and mass extinction in the fossil record, including aclose examination of three major mass extinction events. It will assess the intensity, selectivity, and trends in the current biodiversity crisis and assess the options and prospects for approaches to mitigating and, ultimately, recovering from this sixth extinction. Change of Department Name: Earth and Planetary Science (Formerly Geologic Sciences).
Last offered: Spring 2023
| Units: 3
| UG Reqs: WAY-SMA
| Repeatable
3 times
(up to 9 units total)
BIO 170:
Taking the Pulse of the Ocean: Innovative Technologies for the Blue Planet (OCEANS 170, OCEANS 270)
This will be an interdisciplinary course focused on the intersection of ocean science, marine biology, engineering and computer science. Students will develop an in-depth understanding of the quantitative and field challenges involved in collecting ocean data and designing ocean instruments. Participants will have the opportunity to work with existing ocean technologies such as autonomous underwater and surface vehicles, biologging devices, drones, echosounders, environmental DNA samplers, ocean buoys, ocean drifters, and remotely operated vehicles that will be housed in the 'Ocean Garage'. They will deploy these instruments to study the interplay between physical, chemical and biological oceanography.
Last offered: Spring 2023
| Units: 3
BIO 172:
Ecological Dynamics: Theory and Applications (BIO 272)
Structured population models with age and phenotypic variation. Integral population models, model fitting and dynamics. Fitness and dynamic heterogeneity. Examples from natural populations (sheep, roe deer, plants, birds). Graduate students will be responsible for additional problem sets. Prerequisites: calculus and linear algebra.
Terms: Spr
| Units: 4
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: BIO 83, and BIO 82 and/or BIO 84.
Terms: Spr
| Units: 3
BIO 173H:
Marine Conservation Biology (BIO 273H, OCEANS 173, OCEANS 173H, OCEANS 273H)
Class can be taken in person or via Zoom. Introduction to the key concepts of ecology and policy relevant to marine conservation issues at the population to ecosystems level. Focus on the origin and maintenance of biodiversity and conservation applications from both the biology and policy perspectives (for example, endangered species, captive breeding, reserve design, habitat fragmentation, ecosystem restoration/rehabilitation). Also includes emerging approaches such as ecosystem-based management, ocean planning, and coupled social-ecological systems. The course will include lectures, readings and discussions of primary literature, and attendance at seminars with visiting scholars. Prerequisite: introductory biology; suggested: a policy and/or introductory ecology course. Students who want to enroll only in the seminar and discussion course (2 units) should register for OCEANS/BIO 173HA. (Graduate students register for BIO/OCEANS 273H.) For information on how to spend spring quarter in residence: https://hopkinsmarinestation.stanford.edu/undergraduate-studies/spring-courses-23-24 (Individual course registration also permitted.) Depending on enrollment numbers, a weekly shuttle to Hopkins or mileage reimbursements for qualifying carpools will be provided; terms and conditions apply.
Terms: Spr
| Units: 3
| UG Reqs: WAY-SMA
| Repeatable
for credit
(up to 99 units total)
BIO 176:
The Developmental Basis of Animal Body Plan Evolution (BIO 276)
Animals are grouped into phyla with defined organizational characteristics such as multicellularity, axis organization, and nervous system organization, as well as morphological novelties such as eyes, limbs and segments. This course explores the developmental and molecular origins of there animal innovations. Offered alternate years. Prerequisites: None.
Last offered: Winter 2020
| Units: 4
BIO 178:
Microbiology Literature (BIO 278)
For advanced undergraduates and first-year graduate students. Critical reading of research literature in prokaryotic genetics and molecular biology. Classic and foundational papers in pathogenesis, bacterial and phage genetics, and molecular biology; recent literature on gene regulation. Diverse experimental approaches: biochemistry, genomics, pathogenesis, and cell biology. Prerequisites: undergraduates must have taken BIO 82 (Genetics) and BIO 83 (Biochemistry). Also recommended: BIO 111, BIO 120, CEE 274. Undergraduate enrollment is limited to Biology or Bioengineering majors in junior or senior year. Co-term or Ph.D. students in basic life sciences departments such as Biology, Bioengineering, and Genetics may enroll in BIO 278 for graduate credit. Enrollment by permission of professor, apply at https://forms.gle/fnBTL58QE8H5H22X8.
Terms: Aut
| Units: 3
BIO 179:
The Science & Practice of Valuing Nature for a Better World (BIO 279, EARTHSYS 179, EARTHSYS 279)
This course explores the science of valuing nature, through two interwoven pathways. One is biophysical, focused on human dependence and impacts on Earth's life-support systems. If well managed, lands, waters, and biodiversity yield a flow of vital benefits that sustain and fulfill human life. We will develop a framework and practical tools for quantifying this stream of benefits from nature to people. The second pathway is social, economic, and philosophical, weaving through concepts of well-being, human development, and conservation and the ethics and effects of their pursuit. We will look back, ahead into the future, and inward, taking a global view and considering diverse cultural perspectives. Our discussions will be situated in the context of the COVID-19 pandemic, movements for racial justice and socioeconomic equity, and efforts to enable people and nature to thrive in cities and countries worldwide. The course is intended for diverse, advanced students, with interests in research and in moving from science to action for a more just and sustainable world. Prerequisite: Basic to intermediate GIS (Geographic Information Systems) skills are necessary. We will help with these, but not teach GIS specifically in class. Basic skills include, for example: working with raster, vector and tabular data; loading rasters, shapefiles, and tables into a GIS; changing the symbology of rasters and shapefiles in your chosen GIS; editing raster and shapefile attribute tables; understanding coordinate systems and how to re-project layers; looking at individual raster cell values; and performing basic raster math.
Terms: Aut
| Units: 1-3
BIO 180:
Microbial Physiology (EARTHSYS 255, EPS 233A, ESS 255)
(Formerly GEOLSCI 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. Change of Department Name: Earth and Planetary Science (Formerly Geologic Sciences).
Last offered: Winter 2023
| 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 182H:
Stanford at Sea (BIO 323H, EARTHSYS 323, ESS 323, OCEANS 182H, OCEANS 323H)
(Graduate students register for 323H.) Five weeks of marine science including oceanography, marine physiology, policy, maritime studies, conservation, and nautical science at Hopkins Marine Station, followed by five weeks at sea aboard a sailing research vessel in the Pacific Ocean. Shore component comprised of three multidisciplinary courses meeting daily and continuing aboard ship. Students develop an independent research project plan while ashore, and carry out the research at sea. In collaboration with the Sea Education Association of Woods Hole, MA. Only 6 units may count towards the Biology major.
Terms: Spr
| Units: 16
| UG Reqs: GER: DB-NatSci, WAY-SMA
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 2022
| Units: 3
| UG Reqs: WAY-AQR, WAY-SMA
BIO 184:
Environmental Humanities: Finding Our Place on a Changing Planet (ENGLISH 140D, SUSTAIN 140)
The rapid degradation of our planet threatens the health and survival of communities and ecosystems around the world. How did we get here? What cultural, philosophical, and ethical challenges underlie the separation of humanity from nature and precipitate unprecedented ecological destruction? How can we make sense of this, and how can we reimagine a more connected future? Through engaging the work of environmental philosophers, cultural ecologists, artists, humanities scholars, Indigenous leaders, and others with land-based knowledge, this course will prompt you to think deeply about humanity's place in the world and explore strategies to change our course. Together, we will explore contrasting cultural paradigms around human-nature relationships and apply learnings to action - including through final projects that involve external audiences in meaningful environmental contemplation or impact.
Last offered: Autumn 2022
| Units: 3
| UG Reqs: WAY-A-II, WAY-ER
BIO 185:
Where the Wild Things Are: The Ecology and Ethics of Conserving Megafauna (DLCL 170, EALC 170, EARTHSYS 170, GLOBAL 170)
Under conditions of global environmental change and mass extinction, how will humanity share the planet with wildlife? This course invites undergraduate students to consider this question under the guidance of two biologists and a literary scholar. We will engage with a range of interdisciplinary scholarship on how humans seek to study, understand, exploit, protect, and empathize with charismatic megafauna. We ask how regional differences in culture, political economy, and ecology shape conservation efforts.
Terms: Win
| Units: 3
| UG Reqs: WAY-ER, WAY-SMA
BIO 186:
Archaeobotany (ARCHLGY 126, ARCHLGY 226, BIO 286)
Archaeobotany, also known as paleoethnobotany, is the study of the interrelationships of plants and humans through the archaeological record. Knowledge and understanding of Archaeobotany sufficient to interpret, evaluate, and understand archaeobotanical data. Dominant approaches in the study of archaeobotanical remains: plant macro-remains, pollen, phytoliths, and starch grains in the identification of diet and environmental reconstruction.
Terms: Win
| Units: 5
| UG Reqs: WAY-SMA
BIO 187:
Mathematical Population Biology (CME 187)
Mathematical models in population biology, in biological areas including demography, ecology, epidemiology, evolution, and genetics. Mathematical approaches include techniques in areas such as combinatorics, differential equations, dynamical systems, linear algebra, probability, and stochastic processes. Math 50 or 60 series is required, and at least two of (Bio 81, Bio 82, Bio 85) are strongly recommended.
Last offered: Winter 2022
| Units: 3
BIO 188:
Systems Biology: Principles of Cell Signaling (BIO 288, CSB 288)
The systems biology set of courses aims to give students an overview of how cells process information to build and replicate themselves as well as respond to extracellular signals and environmental changes. The techniques used and discussed in detail are those currently utilized in modern quantitative cell biology. This course in the systems biology set aims to provide an understanding of the principles of cell signaling as applied to natural and synthetic biological circuits. As a primary example of naturally occurring signaling circuits, we will consider in detail the pathway responsible for controlling cell division in response to intra- and extra-cellular signals. The class will cover classic and current techniques for the genetic analysis of the key regulatory circuits governing the control of cell division. Specific topics include tractable model organisms; growth control; and irreversible biochemical switches. The class will be based on a weekly lecture followed by the analysis of classic and current primary literature as well as basic concepts in nonlinear dynamics.
Terms: Aut
| Units: 3
BIO 189:
Emergent and Re-Emergent Viruses as a Global Threat to Human Health (BIO 289)
The goal of the course "Emergent and re-emergent viruses as a global threat to human health"is to provide a holistic vision and a background on the biology, natural history and spread of emerging viruses with emphasis on arboviruses, including the genetic variability of the viruses and their interaction with vectors, reservoirs and human hosts. Strategies for vector control, prophylactics, treatments and social impact will be discussed as well as current and new tools for diagnostics.
Last offered: Spring 2022
| Units: 1
BIO 190:
Geomicrobiology (EARTHSYS 158, EARTHSYS 258, ESS 158, ESS 258)
How microorganisms shape the geochemistry of the Earth's crust including oceans, lakes, estuaries, subsurface environments, sediments, soils, mineral deposits, and rocks. Topics include mineral formation and dissolution; biogeochemical cycling of elements (carbon, nitrogen, sulfur, and metals); geochemical and mineralogical controls on microbial activity, diversity, and evolution; life in extreme environments; and the application of new techniques to geomicrobial systems. Recommended: introductory chemistry and microbiology such as CEE 274A.
| Units: 3
| UG Reqs: WAY-SMA
BIO 191:
Evolutionary Genomics (BIO 332)
Half of the class will be reading/presenting classic and modern papers relevant to evolutionary genomics, in a "journal club" format. We will cover a broad range of topics, methods, and species. The other half will be devoted to evolutionary genomic data analysis: pairs of students will choose a data set (either their own data or published data) and a specific question, and then work throughout the quarter to answer their question.
Terms: Win
| Units: 3
BIO 193:
Interdisciplinary Approaches to Human Health Research (BIOE 193, CHEM 193, CHEMENG 193)
For undergraduate students participating in the Stanford ChEM-H Undergraduate Scholars Program. This course will expose students to interdisciplinary research questions and approaches that span chemistry, engineering, biology, and medicine. Focus is on the development and practice of scientific reading, writing, and presentation skills intended to complement hands-on laboratory research. Students will read scientific articles, write research proposals, make posters, and give presentations.
Last offered: Spring 2020
| Units: 1
| Repeatable
11 times
(up to 11 units total)
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. May be repeat for credit. More information can be found at visit https://web.stanford.edu/~suemcc/TSR/.
Terms: Aut
| Units: 3
| Repeatable
2 times
(up to 6 units total)
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. May be repeat for credit. More information can be found at visit https://web.stanford.edu/~suemcc/TSR/.
Terms: Win
| Units: 3
| UG Reqs: WAY-CE
| Repeatable
2 times
(up to 6 units total)
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. May be repeat for credit. More information can be found at visit https://web.stanford.edu/~suemcc/TSR/.
Terms: Spr
| Units: 3
| UG Reqs: WAY-CE
| Repeatable
2 times
(up to 6 units total)
BIO 197:
Ethics in the Anthropocene (BIO 313, SUSTAIN 331)
Today, in the Anthropocene, humankind impacts the environment on a massive scale, with severe outcomes for species, ecosystems, and landscapes. The consequences of this impact raise many ethical questions, with new dilemmas forcing us to consider new moral values and re-consider old ones. In this course, we will become acquainted with environmental and conservation ethics and philosophy, and acquire the toolkit of concepts and ideas that will allow us to tackle the current environmental ethical debates. We will explore the role of ethics in the environmental and conservation sciences by discussing the philosophical foundations for moral values in the Anthropocene, as well as by examining practical current-day issues, such as reintroductions, invasive species and conservation advocacy.
| Units: 1
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: ;
Bergmann, D. (PI);
Block, B. (PI);
Block, S. (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);
Feldman, J. (PI);
Feldman, M. (PI);
Fernald, R. (PI);
Field, C. (PI);
Fraser, H. (PI);
Frydman, J. (PI);
Fukami, T. (PI);
Gilly, W. (PI);
Goldbogen, J. (PI);
Gordon, D. (PI);
Gozani, O. (PI);
Hadly, E. (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);
Mordecai, E. (PI);
Morrison, A. (PI);
Mudgett, M. (PI);
Nelson, W. (PI);
O'Connell, L. (PI);
Palumbi, S. (PI);
Peay, K. (PI);
Petrov, D. (PI);
Pritchard, J. (PI);
Red-Horse, K. (PI);
Rosenberg, N. (PI);
Sapolsky, R. (PI);
Schnitzer, M. (PI);
Seawell, P. (PI);
Shatz, C. (PI);
Shen, K. (PI);
Simon, M. (PI);
Skotheim, J. (PI);
Spormann, A. (PI);
Stearns, T. (PI);
Tessier-Lavigne, M. (PI);
Thompson, S. (PI);
Ting, A. (PI);
Tuljapurkar, S. (PI);
Vitousek, P. (PI);
Walbot, V. (PI);
Turner, K. (GP)
BIO 198X:
Out-of-Department Directed Reading
Individually arranged under the supervision of members of the faculty. Credit for work arranged with out-of-department faculty is restricted to Biology majors and requires department approval. See 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);
Crowder, L. (PI);
Cyert, M. (PI);
Daily, G. (PI);
Denny, M. (PI);
Dirzo, R. (PI);
Ehrlich, P. (PI);
Feldman, M. (PI);
Fernald, R. (PI);
Field, C. (PI);
Fraser, H. (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);
Klein, R. (PI);
Kopito, R. (PI);
Lipsick, J. (PI);
Long, S. (PI);
Lowe, C. (PI);
Luo, L. (PI);
McConnell, S. (PI);
Micheli, F. (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);
Simon, M. (PI);
Singh, M. (PI);
Skotheim, J. (PI);
Somero, G. (PI);
Thompson, S. (PI);
Tuljapurkar, S. (PI);
Vitousek, P. (PI);
Walbot, V. (PI);
Yang, F. (PI)
BIO 199:
Undergraduate Research
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: ;
Barnes, C. (PI);
Bergmann, D. (PI);
Block, B. (PI);
Block, S. (PI);
Burlacot, A. (PI);
Chen, X. (PI);
Cremer, J. (PI);
Cyert, M. (PI);
Daily, G. (PI);
Daru, B. (PI);
Dinneny, J. (PI);
Dirzo, R. (PI);
Dixon, S. (PI);
Feldman, J. (PI);
Feldman, M. (PI);
Field, C. (PI);
Fraser, H. (PI);
Frydman, J. (PI);
Fukami, T. (PI);
Gordon, D. (PI);
Gozani, O. (PI);
Hadly, E. (PI);
Heller, H. (PI);
Hynes, M. (PI);
Klein, R. (PI);
Kopito, R. (PI);
Long, S. (PI);
Lowe, C. (PI);
Luo, L. (PI);
McConnell, S. (PI);
Mordecai, E. (PI);
Morrison, A. (PI);
Mudgett, M. (PI);
O'Connell, L. (PI);
Palumbi, S. (PI);
Peay, K. (PI);
Petrov, D. (PI);
Pritchard, J. (PI);
Red-Horse, K. (PI);
Rosenberg, N. (PI);
Sapolsky, R. (PI);
Schnitzer, M. (PI);
Schumer, M. (PI);
Sharaf, N. (PI);
Shatz, C. (PI);
Shen, K. (PI);
Simon, M. (PI);
Skotheim, J. (PI);
Stearns, T. (PI);
Tessier-Lavigne, M. (PI);
Thompson, S. (PI);
Ting, A. (PI);
Tuljapurkar, S. (PI);
Vitousek, P. (PI);
Walbot, V. (PI);
Turner, K. (GP)
BIO 199A:
The Independent Capstone in Biology
Seniors in Biology may undertake an independent capstone project through the Independent Capstone in Biology course series, BIO 199 A, B, C. Such projects might involve creative works, research or business internships, travel-based study, teaching, or community service. Examples include the production of a teaching or business plan, a film or podcast, or a public education campaign. The Independent Capstone in Biology is best suited for those students who wish to complete their projects independently, without close peer support and collaboration, while continuing to benefit from project mentorship. Satisfies WIM in Biology.
Terms: Spr
| Units: 3
| Repeatable
2 times
(up to 4 units total)
BIO 199W:
Senior Honors Thesis: How to Effectively Write About Scientific Research
The goal of this class is to support students in developing effective scientific communication skills. It is designed to serve students working to complete a thesis based on a research project, often for Honors. In this class, students will craft elevator pitches, create and improve each section of the thesis, and practice the presentation of scientific information in the context of their own research project. Emphasis will be on building and practicing the skills for 1) completing your thesis, poster and preparing for presentation of the project and 2) gaining a conceptual understanding of effective scientific writing and communication that will be applicable more broadly. Satisfies the WIM requirement in Biology.
Terms: Win
| Units: 3
BIO 199X:
Out-of-Department Undergraduate Research
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: ;
Airan, R. (PI);
Andrews, J. (PI);
Appel, E. (PI);
Artandi, S. (PI);
Barna, M. (PI);
Beachy, P. (PI);
Bergmann, D. (PI);
Bertozzi, C. (PI);
Bhalla, V. (PI);
Bhutani, N. (PI);
Bintu, L. (PI);
Blau, H. (PI);
Blish, C. (PI);
Block, B. (PI);
Block, S. (PI);
Bollyky, P. (PI);
Brunet, A. (PI);
Chang, H. (PI);
Chen, L. (PI);
Chen, X. (PI);
Cheng, A. (PI);
Chu, S. (PI);
Clandinin, T. (PI);
Covert, M. (PI);
Crowder, L. (PI);
Cui, B. (PI);
Cyert, M. (PI);
Daily, G. (PI);
Darian-Smith, C. (PI);
Dassama, L. (PI);
Davis, M. (PI);
Deisseroth, K. (PI);
Demirci, U. (PI);
Denny, M. (PI);
Dionne, J. (PI);
Dirzo, R. (PI);
Dixon, S. (PI);
Du Bois, J. (PI);
Dunbar, R. (PI);
Egan, E. (PI);
Ehrlich, P. (PI);
Feldman, J. (PI);
Feldman, M. (PI);
Felsher, D. (PI);
Fendorf, S. (PI);
Fernald, R. (PI);
Field, C. (PI);
Fire, A. (PI);
Fraser, H. (PI);
Frydman, J. (PI);
Fuller, M. (PI);
Garcia, C. (PI);
George, P. (PI);
Giardino, W. (PI);
Gifford, C. (PI);
Gilly, W. (PI);
Goldbogen, J. (PI);
Goldstein-Piekarski, A. (PI);
Gordon, D. (PI);
Gotlib, I. (PI);
Gozani, O. (PI);
Graves, E. (PI);
Grusky, D. (PI);
Gurtner, G. (PI);
Hadly, E. (PI);
Hallmayer, J. (PI);
Hanawalt, P. (PI);
Heifets, B. (PI);
Heller, H. (PI);
Heller, S. (PI);
Helms, J. (PI);
Huang, K. (PI);
Jarosz, D. (PI);
Jones, P. (PI);
Khavari, P. (PI);
Khosla, C. (PI);
Kim, P. (PI);
Kim, S. (PI);
Kirkegaard, K. (PI);
Knowles, J. (PI);
Knutson, B. (PI);
Kopito, R. (PI);
Kuo, C. (PI);
Lee, C. (PI);
Levitt, M. (PI);
Li, L. (PI);
Long, J. (PI);
Long, S. (PI);
Longaker, M. (PI);
Longo, F. (PI);
Lowe, C. (PI);
Luby, S. (PI);
Luo, L. (PI);
MacIver, M. (PI);
Mackall, C. (PI);
Madison, D. (PI);
Majeti, R. (PI);
Malenka, R. (PI);
Martinez, O. (PI);
McConnell, S. (PI);
Micheli, F. (PI);
Mochly-Rosen, D. (PI);
Monack, D. (PI);
Monje-Deisseroth, M. (PI);
Morrison, A. (PI);
Mudgett, M. (PI);
Nadeau, K. (PI);
Napel, S. (PI);
Negrin, R. (PI);
Nelson, W. (PI);
Newman, A. (PI);
Nguyen, M. (PI);
Norcia, A. (PI);
O'Brien, L. (PI);
O'Connell, L. (PI);
Oro, A. (PI);
Palmer, T. (PI);
Palumbi, S. (PI);
Pasca, S. (PI);
Payne, J. (PI);
Petrov, D. (PI);
Pitteri, S. (PI);
Plant, G. (PI);
Pollack, J. (PI);
Porteus, M. (PI);
Prince, D. (PI);
Pringle, J. (PI);
Pritchard, J. (PI);
Puglisi, J. (PI);
Qi, S. (PI);
Quertermous, T. (PI);
Rankin, E. (PI);
Raymond, J. (PI);
Red-Horse, K. (PI);
Reiss, A. (PI);
Relman, D. (PI);
Rohatgi, R. (PI);
Rosenberg, N. (PI);
Sage, J. (PI);
Sapolsky, R. (PI);
Schnitzer, M. (PI);
Schuele, B. (PI);
Shamloo, M. (PI);
Sharaf, N. (PI);
Shatz, C. (PI);
Shen, K. (PI);
Simon, M. (PI);
Skotheim, J. (PI);
Snyder, M. (PI);
Soltesz, I. (PI);
Stearns, T. (PI);
Steinberg, G. (PI);
Stevenson, D. (PI);
Straight, A. (PI);
Sudhof, T. (PI);
Svensson, K. (PI);
Tan, L. (PI);
Tawfik, V. (PI);
Thompson, S. (PI);
Ting, A. (PI);
Tuljapurkar, S. (PI);
Utz, P. (PI);
Vitousek, P. (PI);
Walbot, V. (PI);
Wang, S. (PI);
Waymouth, R. (PI);
Weissman, I. (PI);
Wender, P. (PI);
Winslow, M. (PI);
Wu, J. (PI);
Wu, S. (PI);
Wyss-Coray, T. (PI);
Yang, F. (PI);
Yang, Y. (PI);
Zhao, H. (PI);
van Rechem, C. (PI);
Dang, V. (GP);
Johnson, S. (GP);
McSwain, R. (GP);
Ramalho, D. (GP)
BIO 201:
Techniques in Environmental Microbiology (ESS 210)
Fundamentals and application of laboratory techniques to study the diversity and activity of microorganisms in environmental samples, including soil, sediment, and water. Emphasis is on culture-independent approaches, including epifluorescence microscopy, extraction and analysis of major biomolecules (DNA, RNA, protein, lipids), stable isotope probing, and metabolic rate measurements. Format will include lectures, laboratory exercises, and discussions. Students will learn how to collect, analyze, and understand common and cutting-edge datasets in environmental microbiology. Permission from instructor is required to enroll as C/NC or for 1-3 units.
Last offered: Spring 2022
| Units: 1-4
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. Instructor permission required. Students interested in taking this course should fill out this application form: https://forms.gle/eEaccJjvhKYKB1R4A
Last offered: Autumn 2022
| 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: Win
| Units: 3
BIO 205:
Microbes and Climate (BIO 105, ESS 122, ESS 222)
Microorganisms drive the cycling of carbon, oxygen, and other nutrients in the earth system. This means that microbes both impact and are impacted by changes in climate. In this reading course, participants will read and present a combination of classic and current papers in the primary literature. Topics will include: the co-evolution of microbial metabolism and the climate system over geological timescales; impacts of current climate change on microbial physiology, community ecology, and ecosystem function; multiple stressors; feedbacks of microbial communities to anthropogenic greenhouse gas emissions; methods for connecting microbial activities to climate dynamics in process models.
Last offered: Autumn 2022
| Units: 1
BIO 206:
Statistical Genomics for Planetary Health: Oceans, Plants, Microbes and Humans (BIODS 228)
Data scientific analysis of genomics data has transformed biology, enabling myriad discoveries with enormous impacts on human and planetary health. Algorithms and statistics are central to knowledge of human and plant genomic variation, to microbiomes and carbon cycling in the ocean. This class will present the important open problems in the above application areas, pose them as statistical problems and explore core, unifying methods that are used to study them. We will cover diverse scientific application areas focusing on unifying ways they can be addressed statistics and informatics including (i) historical and computer-scientific approaches to addressing these problems where analysis begins with assembling and or aligning to a set of reference genomes (ii) 'statistics-first' approaches that operate on raw sequencing data to perform statistical inference for discovery. This class will present challenges and opportunities in using new methods that do not require a reference to illustrate how the planetary ecosystem can be investigated from a statistics-first perspective: from studies of microbial and plant life to humans. Motivation will be driven by current open and critical problems in planetary health, microbiome research and examples from human genomics. We will investigate statistical and informatic methods that can be used to address these problems including generalized linear models, Pearson's chi-square, permutation testing and present scientific examples/case studies where these tests fail to control the statistical level. Lectures will be pre-recorded with mandatory in-class discussions and problem sessions in class. Evaluation will be based on completion of ungraded problem sets with the major evaluation will be class projects.
| 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.
Last offered: Spring 2022
| Units: 2
| Repeatable
2 times
(up to 4 units total)
BIO 210:
The Chromatin-Regulated 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 BIO 83 or consent of instructor.
Last offered: Spring 2022
| Units: 3
BIO 211:
Proteostasis: From Basic Principles to Aging and Neurodegeneration
Proteostasis, or protein homeostasis, is emerging as the central cellular process controlling the stability, function, and quality control of the proteome. The proteostasis machinery maintains the function of destabilized and mutant proteins, assists the degradation of damaged and aggregated proteins, and monitors the health of the proteome, adjusting it in response to environmental or metabolic stresses. Most mutations linked to disease act by challenging the structure, stability or function of proteins. Thus, understanding and manipulating proteostasis could hold the key for the therapeutic treatment of a wide range of diseases. Cellular proteostasis declines during aging, leading to increased prevalence of late-onset aggregation-linked amyloid diseases implicated in many devastating neurodegenerative diseases (e.g. Alzheimer's, Parkinson's, ALS). We will discuss basic and translational advances of the Proteostasis field and their potential to lead to novel therapies for a wide range of diseases including neurodegeneration, cancer, cardiomyopathy, cystic fibrosis, cataract, metabolic deficiencies and other chronic maladies. Topics to be Covered: 1. Protein Folding and the Molecular Chaperone Concept; 2. Mechanisms and Principle of Molecular Chaperone Action; 3. What is Proteostasis: protein folding and homeostasis in vivo; 4. The Ubiquitin Proteasome pathway and Protein Quality Control; 5. Protein Aggregation, Amyloids and Neurodegenerative Disease; 6. Proteostasis dysfunction and ageing; 7. Therapeutics targeting "proteostasis."
Terms: Win
| Units: 3
| Repeatable
2 times
(up to 6 units total)
BIO 212:
Modern Coexistence Theory
Discuss papers that explain the theory and application of the CET. A list of papers will be distributed.
Last offered: Spring 2022
| Units: 1
BIO 214:
Advanced Cell Biology (BIOC 224, MCP 221)
For Ph.D. students. Taught from the current literature on cell structure, function, and dynamics. Topics include complex cell phenomena such as cell division, apoptosis, signaling, compartmentalization, transport and trafficking, motility and adhesion, and differentiation. Weekly reading of current papers from the primary literature. Advanced undergraduates may participate with the permission of the Course Director.
Terms: Win
| Units: 3
BIO 218:
Visualizing Biomolecules (CHEM 287)
(This course is for graduate students only. ) Leveraging high-resolution structural techniques to visualize and understand the function and mechanisms of biological molecules, with an emphasis on proteins. The course covers the theory of modern x-ray diffraction and electron microscopy for macromolecules, provides hands-on experimentation with both techniques and presents case studies from the literature to highlight how these techniques can be leveraged to reveal the mechanisms of action of some of nature's most powerful catalysts.
Terms: Aut
| Units: 5
BIO 220:
Integrative and Experimental Microbiology (BIO 120)
To survive, grow, and reproduce, organisms coordinate different molecular processes so they can use available resources and cope with environmental conditions. This laboratory course explores molecular and cellular integration in bacteria. Experiments include the quantification of growth, mutational screens and mutant analysis, gene cloning, and measuring/engineering gene-expression. These "wet lab" approaches will be combined with "dry lab" approaches to analyze experimental findings and explore further the link between molecular processes, cell-physiology, and ecology. Prerequisite: MATH 51 or MATH 19, 20,21. Recommended: microbiology (e.g. BIO 62 or 162) and molecular biology/biochemistry/genetics courses (e.g. BIO 82 or 83). Enrollment via Application: https://forms.gle/etRHRhhaRJxUMyNW9
Terms: Spr
| Units: 3
| Repeatable
1 times
(up to 3 units total)
BIO 221:
Ornithology (BIO 121)
Advanced undergraduate survey of ornithology, introducing students to the biology of birds and giving them to tools to use birds as model systems for research. Topics will include avian evolution, physiology, adaptations, behavior, and ecology. Focus throughout on identification of California birds and applications to current bird conservation issues. Course will include lectures and a field component which will expose students to standard avian research techniques such as mistnetting, banding, and point count surveys. Prerequisite: BIO 81 or BIO 105A/B or instructor approval.
Terms: Spr
| Units: 3
BIO 222:
Exploring Neural Circuits
Seminar. This course focuses on the logic of how neural circuits process information and control behavior, as well as 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, motor control, and cognitive function; 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: https://luolab.stanford.edu/teaching. Please submit by the last week of the winter quarter. Recommended: background in neuroscience.
Terms: Spr
| Units: 3
BIO 223:
Stochastic and Nonlinear Dynamics (APPPHYS 223, BIOE 213, PHYSICS 223)
Theoretical analysis of dynamical processes: dynamical systems, stochastic processes, and spatiotemporal dynamics. Motivations and applications from biology and physics. Emphasis is on methods including qualitative approaches, asymptotics, and multiple scale analysis. Prerequisites: ordinary and partial differential equations, complex analysis, and probability or statistical physics.
Terms: Aut
| Units: 3
BIO 224:
Plant Ecology & Evolution in Arid Climates (BIO 164, EARTHSYS 224)
Understanding responses of plants to climate change is paramount to protect our ecosystems. In this course, we will review classical work on fundamental concepts of plant biology and evolutionary ecology in arid climates. We will study plant biodiversity patterns in arid climates, we will collect and investigate plants and their ecophysiological stress coping strategies, and we will learn how to use genomics to understand plant adaptation. The course will introduce some new technologies, such as bioinformatic tools, DNA sequencing, biodiversity databases, etc. And we will have field trips to Jasper Ridge and other ecosystems to see living examples across the California landscape. Enrollment limited; application required. Apply at https://docs.google.com/forms/d/e/1FAIpQLScWPTN4HI-IUoFhgOMaXwFVpGZnOB5-9O0qufaObYf5iAK6KA/viewform.
Last offered: Spring 2023
| 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 2021
| Units: 3
BIO 228:
Evolution of Terrestrial Ecosystems (BIO 148, EARTHSYS 128, EPS 128, EPS 228)
(Formerly GEOLSCI 128 and 228) The what, when, where, and how do we know it regarding life on land through time. Fossil plants, fungi, invertebrates, and vertebrates (yes, dinosaurs) are all covered, including how all of those components interact with each other and with changing climates, continental drift, atmospheric composition, and environmental perturbations like glaciation and mass extinction. The course involves both lecture and lab components. Graduate students registering at the 200-level are expected to write a term paper, but can opt out of some labs where appropriate. Change of Department Name: Earth and Planetary Science (Formerly Geologic Sciences).
Last offered: Winter 2023
| Units: 4
BIO 229:
Fundamentals and Frontiers in Plant Biology (BIO 129)
This course will serve as a primer for all levels of graduate, co-term, and upper-level undergraduates interested in learning about the fundamental aspects of plant biology, the latest advances in tools, techniques, and theories that link basic science with translational science and applications for solving major societal challenges of today and tomorrow. In addition, this course will serve to introduce the breadth of plant research on campus and help solidify a cohort of students interested in plant biology.
Last offered: Spring 2022
| Units: 3
| Repeatable
2 times
(up to 6 units total)
BIO 230:
Cellular and Molecular Immunology: An Introductory Course (IMMUNOL 200, MI 200)
Mechanisms of immune responses in health and disease. Innate and adaptive immunity; development of the immune system; molecular biology, structure, and function of antibodies and T-cell receptors; cellular basis and regulation of immune responses; infectious diseases and vaccines; allergy, inflammation, and autoimmunity. COVID-19 will be featured as a major example. Lectures and discussion in class and in sections. For upper class undergraduate and graduate students who have not had an introductory immunology course. Prerequisites for undergraduates: Biology Core, Human Biology Core, or BIO 83 and 86, or consent of instructor. For graduate students: College-level molecular biology, biochemistry, and cell biology, or consent of instructor.
Terms: Aut
| Units: 4
BIO 231:
Structural Equation Modeling for Ecologists
We will focus on learning to use structural equation modeling (SEM) as a technique for ecological inference. Class will include short lectures, paper discussions, and SEM coding workshops in R. IMPORTANT NOTE: class meets in Gilbert 115.
Last offered: Autumn 2021
| Units: 1
BIO 232:
Advanced Imaging Lab in Biophysics (APPPHYS 232, BIO 132, BIOE 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, basic cell biology, and consent of instructor.
Terms: Spr
| Units: 4
BIO 233:
Genetics, Development and Evolution of Pigmentation
Genetics, development and evolution of pigmentation.
Last offered: Autumn 2022
| Units: 2
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 the 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. All students will be expected to conduct a literature research exercise leading to a written report, addressing a topic of their choosing, derived from any of the themes discussed in class.
Terms: Spr
| Units: 3
BIO 236:
Macroevolution (BIO 136, EPS 136, EPS 236)
(Formerly GEOLSCI 136 and 236) The course will focus on the macroevolution of animals. We will be exploring how paleobiology and developmental biology/genomics have contributed to our understanding of the origins of animals, and how patterns of evolution and extinction have shaped the diversity of animal forms we observe today. Change of Department Name: Earth and Planetary Science (Formerly Geologic Sciences).
Terms: Spr
| Units: 3
BIO 237:
The Sixth Extinction (and the Other Five) (BIO 169, EARTHSYS 127A, EARTHSYS 227A, EPS 137, EPS 237)
(Formerly GEOLSCI 137 and 237) Are we living through Earth's sixth major mass extinction event? The course will address the causes and consequences of extinction. It will review current understanding of background and mass extinction in the fossil record, including aclose examination of three major mass extinction events. It will assess the intensity, selectivity, and trends in the current biodiversity crisis and assess the options and prospects for approaches to mitigating and, ultimately, recovering from this sixth extinction. Change of Department Name: Earth and Planetary Science (Formerly Geologic Sciences).
Last offered: Spring 2023
| Units: 3
| Repeatable
3 times
(up to 9 units total)
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 81, 85 recommended.
Terms: Win
| Units: 4
BIO 240:
Ecosystem Ecology and Biogeochemistry (BIO 147, EARTHSYS 147, EARTHSYS 247)
An introduction to ecosystem ecology and terrestrial biogeochemistry. This course will focus on the dynamics of carbon and other biologically essential elements in the Earth System, on spatial scales from local to global. Prerequisites: Biology 117, Earth Systems 111, or graduate standing.
Last offered: Autumn 2021
| Units: 3
BIO 243:
Quantitative Methods for Marine Ecology and Conservation (BIO 143, CEE 164, CEE 264H, EARTHSYS 143H, EARTHSYS 243H, OCEANS 143)
NOTE: This course will be taught in-person on main campus, in hybrid format with Zoom options. The goal of this course is to learn the foundations of ecological modeling with a specific (but not exclusive) focus on marine conservation and sustainable exploitation of renewable resources. Students will be introduced to a range of methods - from basic to advanced - to characterize population structure, conduct demographic analyses, estimate extinction risk, identify temporal trends and spatial patterns, quantify the effect of environmental determinants and anthropogenic pressures on the dynamics of marine populations, describe the potential for adaptation to climate change. This course will emphasize learning by doing, and will rely heavily on practical computer laboratories, in R and/or Phyton, based on data from our own research activities or peer reviewed publications. Students with a background knowledge of statistics, programming and calculus will be most welcome. Formally BIOHOPK 143H and 243H.
Terms: Win
| 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. Prerequisites: Biology core or BIO 82, 85 or graduate standing in any department, and consent of instructor.
Terms: Win
| Units: 4
BIO 245:
Animal Behavior (BIO 145)
Animal behavior with an emphasis on social and collective behavior. How do animals interact with each other and the rest of the world around them? This is a project-based course in a seminar format, including class discussion of journal articles, and independent research projects based on observing the behavior of animals on campus. Prerequisites suggested: Biology or Human Biology core or BIO 81 and 85 or consent of instructor; BIO/ES 30. Recommended: some background in statistics.
Terms: Win
| Units: 3
BIO 247:
Genomic approaches to the study of human disease (BIO 127, GENE 247)
This course will cover a range of genetic and genomic approaches to studying human phenotypic variation and disease. We will discuss the genetic basis of Mendelian and complex diseases, as well as clinical applications including prenatal testing, and pediatric and cancer diagnostics. The course will include lectures as well as critical reading and discussion of the primary literature. Prerequisite: BIO 82 or equivalent. Open to advanced undergraduate students.
Terms: Win
| Units: 3
BIO 249:
The Neurobiology of Sleep (BIO 149, HUMBIO 161, PSYC 149, PSYC 261)
The neurochemistry and neurophysiology of changes in brain activity and conscious awareness are associated with changes in the sleep/wake state. Behavioral and neurobiological phenomena include sleep regulation, sleep homeostasis, circadian rhythms, sleep disorders, sleep function, and the molecular biology of sleep. Preference to seniors and graduate students.
Terms: Win
| Units: 4
BIO 251:
Quantitative Evolutionary Dynamics and Genomics (APPPHYS 237)
The genomics revolution has fueled a renewed push to model evolutionary processes in quantitative terms. This course will provide an introduction to quantitative evolutionary modeling through the lens of statistical physics. Topics will range from the foundations of theoretical population genetics to experimental evolution of laboratory microbes. Course work will involve a mixture of pencil-and-paper math, writing basic computer simulations, and downloading and manipulating DNA sequence data from published datasets. This course is intended for upper level physics and math students with no biology background, as well as biology students who are comfortable with differential equations and probability.
Terms: Spr
| Units: 3
BIO 254:
Principles of Neurobiology (NBIO 254)
For graduate students. Includes lectures with BIO 154 and additional paper discussion sections. Principles and mechanisms in the organization and functions of the nervous system. Topics: neuronal communication, sensory and motor systems, innate behaviors, learning and memory, brain disorders, and evolution of the nervous system.
Last offered: Winter 2023
| Units: 3-5
BIO 255:
Cell and Developmental Biology of Plants (BIO 155)
In this course we will learn how plants are built at different organizational scales from the cell, tissue, organ and organ system level. We will also learn about the experimental methods used to study plants at these different organizational levels and how to interpret and evaluate experiments that use such methods. Finally, advances in genetic engineering will be discussed as a means of manipulating the form and function of plants for sustainable agriculture. Broadly relevant skills that will be cultivated in the course include: evaluating primarily literature, identifying gaps in knowledge, formulating research questions and designing new experimental strategies. Prerequisites: BIO 80 series or equivalent.
Last offered: Autumn 2022
| Units: 3
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. Prerequisites: BIO 82, 83, 84, 86.
Last offered: Autumn 2022
| Units: 4
BIO 265:
Quantitative Approaches in Modern Biology (BIO 165)
Modern research approaches tightly integrate experimentation with data analysis and mathematical modeling to provide unprecedented insights into the organization and functioning of living systems. This course explores the quantitative basis of major cellular processes and their coordination to form a cohesive physiological entity that is capable of rapid growth and acclimation to changing environments. Weekly lectures will be accompanied by 'dry lab sessions' in which students analyze experimental data sets and discuss the challenges of accomplishing rigorous and reproducible research. As such, students will actively develop a fundamental skill set of quantitative biology which includes knowledge in coding, dynamical systems modeling, and statistics. Assumes basic (but not advanced) familiarity with math, e.g. MATH51. Enrollment by permission of the professor, apply at https://forms.gle/j6ocJs8fQFPK1GGLA.
Terms: Win
| Units: 3
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.This class is open to both graduate and undergraduate students, but requires sufficient backgrounds in college level genetics, cell biology and biochemistry. Undergraduates who are interested are required to contact the course director first.
Last offered: Winter 2020
| Units: 4
BIO 268:
Statistical and Machine Learning Methods for Genomics (BIOMEDIN 245, CS 373, 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.
Last offered: Winter 2020
| Units: 3
BIO 269:
Comparative Single-cell Genomics in the Ocean (BIOE 269)
The goal of the course is to provide students with hands-on experience in applying single-cell sequencing technology to examine marine animals with cellular resolution, both at the bench and on computers. Throughout the course, students learn how to collect animals, dissect and dissociate tissues, generate single-cell sequencing libraries, process and analyze their own data, and compare cell types across animals using the computational pipelines. This pipeline is optimized to study organisms without extensive prior knowledge and provides students with a valuable set of tools for future work in this field. This course uses a diverse set of animals in order to study the conservation and divergence of cell types and their gene regulatory programs across the animal kingdom. The course includes lectures on Mondays, and web and dry lab components, which have flexible schedules. Pre-requite: BioE219 (recommended for engineering students) or instructor consent.
Last offered: Summer 2023
| Units: 3
BIO 272:
Ecological Dynamics: Theory and Applications (BIO 172)
Structured population models with age and phenotypic variation. Integral population models, model fitting and dynamics. Fitness and dynamic heterogeneity. Examples from natural populations (sheep, roe deer, plants, birds). Graduate students will be responsible for additional problem sets. Prerequisites: calculus and linear algebra.
Terms: Spr
| Units: 4
BIO 273A:
Environmental Microbiology I (CEE 274A, CHEMENG 174, CHEMENG 274)
Basics of microbiology and biochemistry. The biochemical and biophysical principles of biochemical reactions, energetics, and mechanisms of energy conservation. Diversity of microbial catabolism, flow of organic matter in nature: the carbon cycle, and biogeochemical cycles. Bacterial physiology, phylogeny, and the ecology of microbes in soil and marine sediments, bacterial adhesion, and biofilm formation. Microbes in the degradation of pollutants. Prerequisites: CHEM 33,CHEM 121 (formerly CHEM 35), and BIOSCI 83, CHEMENG 181, or equivalents.
Last offered: Autumn 2020
| Units: 3
BIO 273B:
Microbial Bioenergy Systems (CEE 274B, CHEMENG 456)
Introduction to microbial metabolic pathways and to the pathway logic with a special focus on microbial bioenergy systems. The first part of the course emphasizes the metabolic and biochemical principles of pathways, whereas the second part is more specifically directed toward using this knowledge to understand existing systems and to design innovative microbial bioenergy systems for biofuel, biorefinery, and environmental applications. There also is an emphasis on the implications of rerouting of energy and reducing equivalents for the fitness and ecology of the organism. Prerequisites: CHEMENG 174 or 181 and organic chemistry, or equivalents.
Last offered: Winter 2020
| Units: 3
BIO 273H:
Marine Conservation Biology (BIO 173H, OCEANS 173, OCEANS 173H, OCEANS 273H)
Class can be taken in person or via Zoom. Introduction to the key concepts of ecology and policy relevant to marine conservation issues at the population to ecosystems level. Focus on the origin and maintenance of biodiversity and conservation applications from both the biology and policy perspectives (for example, endangered species, captive breeding, reserve design, habitat fragmentation, ecosystem restoration/rehabilitation). Also includes emerging approaches such as ecosystem-based management, ocean planning, and coupled social-ecological systems. The course will include lectures, readings and discussions of primary literature, and attendance at seminars with visiting scholars. Prerequisite: introductory biology; suggested: a policy and/or introductory ecology course. Students who want to enroll only in the seminar and discussion course (2 units) should register for OCEANS/BIO 173HA. (Graduate students register for BIO/OCEANS 273H.) For information on how to spend spring quarter in residence: https://hopkinsmarinestation.stanford.edu/undergraduate-studies/spring-courses-23-24 (Individual course registration also permitted.) Depending on enrollment numbers, a weekly shuttle to Hopkins or mileage reimbursements for qualifying carpools will be provided; terms and conditions apply.
Terms: Spr
| Units: 3
| Repeatable
for credit
(up to 99 units total)
BIO 274S:
Hopkins Microbiology Course (CEE 274S, ESS 253S, OCEANS 274)
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. Formerly BIOHOPK 274H.
Last offered: Summer 2021
| Units: 3-12
| Repeatable
for credit
BIO 276:
The Developmental Basis of Animal Body Plan Evolution (BIO 176)
Animals are grouped into phyla with defined organizational characteristics such as multicellularity, axis organization, and nervous system organization, as well as morphological novelties such as eyes, limbs and segments. This course explores the developmental and molecular origins of there animal innovations. Offered alternate years. Prerequisites: None.
Last offered: Winter 2022
| Units: 4
BIO 278:
Microbiology Literature (BIO 178)
For advanced undergraduates and first-year graduate students. Critical reading of research literature in prokaryotic genetics and molecular biology. Classic and foundational papers in pathogenesis, bacterial and phage genetics, and molecular biology; recent literature on gene regulation. Diverse experimental approaches: biochemistry, genomics, pathogenesis, and cell biology. Prerequisites: undergraduates must have taken BIO 82 (Genetics) and BIO 83 (Biochemistry). Also recommended: BIO 111, BIO 120, CEE 274. Undergraduate enrollment is limited to Biology or Bioengineering majors in junior or senior year. Co-term or Ph.D. students in basic life sciences departments such as Biology, Bioengineering, and Genetics may enroll in BIO 278 for graduate credit. Enrollment by permission of professor, apply at https://forms.gle/fnBTL58QE8H5H22X8.
Terms: Aut
| Units: 3
BIO 279:
The Science & Practice of Valuing Nature for a Better World (BIO 179, EARTHSYS 179, EARTHSYS 279)
This course explores the science of valuing nature, through two interwoven pathways. One is biophysical, focused on human dependence and impacts on Earth's life-support systems. If well managed, lands, waters, and biodiversity yield a flow of vital benefits that sustain and fulfill human life. We will develop a framework and practical tools for quantifying this stream of benefits from nature to people. The second pathway is social, economic, and philosophical, weaving through concepts of well-being, human development, and conservation and the ethics and effects of their pursuit. We will look back, ahead into the future, and inward, taking a global view and considering diverse cultural perspectives. Our discussions will be situated in the context of the COVID-19 pandemic, movements for racial justice and socioeconomic equity, and efforts to enable people and nature to thrive in cities and countries worldwide. The course is intended for diverse, advanced students, with interests in research and in moving from science to action for a more just and sustainable world. Prerequisite: Basic to intermediate GIS (Geographic Information Systems) skills are necessary. We will help with these, but not teach GIS specifically in class. Basic skills include, for example: working with raster, vector and tabular data; loading rasters, shapefiles, and tables into a GIS; changing the symbology of rasters and shapefiles in your chosen GIS; editing raster and shapefile attribute tables; understanding coordinate systems and how to re-project layers; looking at individual raster cell values; and performing basic raster math.
Terms: Aut
| Units: 1-3
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 2022
| Units: 3
BIO 286:
Archaeobotany (ARCHLGY 126, ARCHLGY 226, BIO 186)
Archaeobotany, also known as paleoethnobotany, is the study of the interrelationships of plants and humans through the archaeological record. Knowledge and understanding of Archaeobotany sufficient to interpret, evaluate, and understand archaeobotanical data. Dominant approaches in the study of archaeobotanical remains: plant macro-remains, pollen, phytoliths, and starch grains in the identification of diet and environmental reconstruction.
Terms: Win
| Units: 5
BIO 287A:
Advanced Topics in Mathematical Evolutionary Biology
Focused examination of specific topics in mathematical evolutionary biology. Course themes may include: mathematical properties of statistics used in human population genetics, mathematics of evolutionary trees, and the intersection of population genetics and phylogenetics.
Terms: Aut
| Units: 3
BIO 288:
Systems Biology: Principles of Cell Signaling (BIO 188, CSB 288)
The systems biology set of courses aims to give students an overview of how cells process information to build and replicate themselves as well as respond to extracellular signals and environmental changes. The techniques used and discussed in detail are those currently utilized in modern quantitative cell biology. This course in the systems biology set aims to provide an understanding of the principles of cell signaling as applied to natural and synthetic biological circuits. As a primary example of naturally occurring signaling circuits, we will consider in detail the pathway responsible for controlling cell division in response to intra- and extra-cellular signals. The class will cover classic and current techniques for the genetic analysis of the key regulatory circuits governing the control of cell division. Specific topics include tractable model organisms; growth control; and irreversible biochemical switches. The class will be based on a weekly lecture followed by the analysis of classic and current primary literature as well as basic concepts in nonlinear dynamics.
Terms: Aut
| Units: 3
BIO 289:
Emergent and Re-Emergent Viruses as a Global Threat to Human Health (BIO 189)
The goal of the course "Emergent and re-emergent viruses as a global threat to human health"is to provide a holistic vision and a background on the biology, natural history and spread of emerging viruses with emphasis on arboviruses, including the genetic variability of the viruses and their interaction with vectors, reservoirs and human hosts. Strategies for vector control, prophylactics, treatments and social impact will be discussed as well as current and new tools for diagnostics.
Last offered: Spring 2022
| Units: 1
BIO 290:
Teaching Practicum in Biology
Open to upper-division undergraduates and graduate students. Practical, supervised teaching experience in a biology lab or lecture course. Training often includes attending lectures, initiating and planning discussion sections, and assisting in the preparation course materials. May be repeated for credit.nPrerequisite: 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);
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);
Grossman, A. (PI);
Hadly, E. (PI);
Hanawalt, P. (PI);
Hekmat-Scafe, D. (PI);
Heller, H. (PI);
Heller, R. (PI);
Imam, J. (PI);
Jacobs-Wagner, C. (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);
Marxmiller, E. (PI);
McConnell, S. (PI);
Micheli, F. (PI);
Miller, J. (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);
Schumer, M. (PI);
Seawell, P. (PI);
Shatz, C. (PI);
Shen, K. (PI);
Simon, M. (PI);
Skotheim, J. (PI);
Stearns, T. (PI);
Thompson, S. (PI);
Tuljapurkar, S. (PI);
Vitousek, P. (PI);
WU, A. (PI);
Walbot, V. (PI);
Wang, Z. (PI);
Watanabe, J. (PI);
Watt, W. (PI);
Turner, K. (GP)
BIO 291:
Development and Teaching of Core Experimental Laboratories
Development and Teaching of Core Experimental LaboratoriesPreparation for teaching the core experimental lab courses (45 and 47). Emphasis is on practicing the lab, speaking, and writing skills. Taken simultaneously while teaching (for BIO 45) or during the previous quarter (for teaching BIO 47). May be repeated for credit. Meeting times TBD.
Terms: Aut, Win
| Units: 1-2
| Repeatable
for credit
BIO 292:
Curricular Practical Training
This course is required for international students who are participating in professional internships in organizations (e.g. research institutes, education, medicine, business, policy) with a focus in the biological sciences. Students will be engaged in on-the-job training under the guidance of experienced, on-site supervisors. This course meets the requirements for curricular practical training (CPT) for students with F-1D/S status. Prior to the internship, students are required to submit a concise report detailing the proposed project and work activities. After the internship, students are required to submit a summary of the work completed, skills learned, and reflection of the professional growth gained as a result of the internship. This course may be repeated for credit. Prerequisite: Qualified offer of employment and consent of advisor.
Terms: Aut, Win, Spr, Sum
| Units: 1-10
| Repeatable
3 times
(up to 10 units total)
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.
Terms: Win
| Units: 3
BIO 296:
Teaching and Learning in Biology
This course provides students teaching in the Department of Biology with basic training, support, and professional development in their teaching roles. Topics include student engagement, assessment, feedback and more. Should be taken concurrently with the first teaching 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: ;
Barnes, C. (PI);
Bergmann, D. (PI);
Block, B. (PI);
Block, S. (PI);
Chen, X. (PI);
Cremer, J. (PI);
Cyert, M. (PI);
Daily, G. (PI);
Daru, B. (PI);
Dinneny, J. (PI);
Dirzo, R. (PI);
Dixon, S. (PI);
Dukes, J. (PI);
Exposito-Alonso, M. (PI);
Feldman, J. (PI);
Feldman, M. (PI);
Field, C. (PI);
Fraser, H. (PI);
Frommer, W. (PI);
Frydman, J. (PI);
Fukami, T. (PI);
Goldbogen, J. (PI);
Gordon, D. (PI);
Gozani, O. (PI);
Hadly, E. (PI);
Heller, H. (PI);
Jacobs-Wagner, C. (PI);
Klein, R. (PI);
Kopito, R. (PI);
Long, S. (PI);
Lowe, C. (PI);
Luo, L. (PI);
McConnell, S. (PI);
Mordecai, E. (PI);
Morrison, A. (PI);
Mudgett, M. (PI);
O'Connell, L. (PI);
Palumbi, S. (PI);
Peay, K. (PI);
Petrov, D. (PI);
Pritchard, J. (PI);
Red-Horse, K. (PI);
Rhee, S. (PI);
Rosenberg, N. (PI);
Sapolsky, R. (PI);
Schnitzer, M. (PI);
Schumer, M. (PI);
Sharaf, N. (PI);
Shatz, C. (PI);
Shen, K. (PI);
Simon, M. (PI);
Skotheim, J. (PI);
Stearns, T. (PI);
Tessier-Lavigne, M. (PI);
Ting, A. (PI);
Tuljapurkar, S. (PI);
Vitousek, P. (PI);
Walbot, V. (PI);
Wang, Z. (PI);
Turner, K. (GP)
BIO 300X:
Out-of-Department Graduate Research
Individual research by arrangement with out-of-department instructors. Master's students: credit for work arranged with out-of-department instructors is restricted to Biology students and requires approved department petition. See http://biohonors.stanford.edu for more information. May be repeated for credit.
Terms: Aut, Win, Spr, Sum
| Units: 1-10
| Repeatable
for credit
Instructors: ;
Abu-Remaileh, M. (PI);
Appel, E. (PI);
Bertozzi, C. (PI);
Bhatt, A. (PI);
Bintu, L. (PI);
Brandman, O. (PI);
Brunet, A. (PI);
Cegelski, L. (PI);
Chaudhuri, O. (PI);
Clandinin, T. (PI);
Curtis, C. (PI);
Diehn, M. (PI);
Endy, D. (PI);
Eshel, N. (PI);
Jackson, P. (PI);
Jarosz, D. (PI);
Khavari, P. (PI);
Kirkegaard, K. (PI);
Knowles, J. (PI);
Krasnow, M. (PI);
Kuo, C. (PI);
Lin, M. (PI);
Long, J. (PI);
Long, S. (PI);
Martinez, N. (PI);
Mochly-Rosen, D. (PI);
Monje-Deisseroth, M. (PI);
Oro, A. (PI);
Prakash, M. (PI);
Relman, D. (PI);
Reticker-Flynn, N. (PI);
Roncarolo, M. (PI);
Rutaganira, F. (PI);
Sage, J. (PI);
Sebastiano, V. (PI);
Sobel, R. (PI);
Straight, A. (PI);
Tessier-Lavigne, M. (PI);
Wang, B. (PI);
Weissman, I. (PI);
Wernig, M. (PI);
Wu, J. (PI);
Wysocka, J. (PI);
Wyss-Coray, T. (PI);
Arzate, M. (GP);
McSwain, R. (GP);
Ramalho, D. (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 is open 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 isopen 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 is open only to Biology PhD students and is not open to auditors.
Terms: Spr
| Units: 1
BIO 305:
Managing Your PhD
The course will focus on 5 themes for effectively managing your PhD: professionalism, scholarship, well-being, community-engagement and career development. We will meet every other week and have an active discussion-based class meeting for 2 hours. At the end of the quarter students and instructors will co-organize a departmental half-day workshop on a particular topic relevant to the topics covered in the class.
Terms: Aut, Spr
| Units: 1
| Repeatable
6 times
(up to 6 units total)
BIO 310:
Current Topics in Cell and Molecular Biology
Required of Cell, Molecular, and Organismal Biology (CMOB) students in their first year of PhD graduate training. This seminar course includes informal presentations of current research projects and results by faculty in the CMOB program.
| Units: 1
BIO 312:
Responsible Conduct in Cellular and Molecular Biology
Required of PhD graduate students in the Cell, Molecular, and Organismal Biology training program. Selected faculty will lead discussion of topics related to responsible conduct of research and ethics, such as conflict of interest, authorship, collaborative research, and data management.
Terms: Spr
| Units: 1
BIO 313:
Ethics in the Anthropocene (BIO 197, SUSTAIN 331)
Today, in the Anthropocene, humankind impacts the environment on a massive scale, with severe outcomes for species, ecosystems, and landscapes. The consequences of this impact raise many ethical questions, with new dilemmas forcing us to consider new moral values and re-consider old ones. In this course, we will become acquainted with environmental and conservation ethics and philosophy, and acquire the toolkit of concepts and ideas that will allow us to tackle the current environmental ethical debates. We will explore the role of ethics in the environmental and conservation sciences by discussing the philosophical foundations for moral values in the Anthropocene, as well as by examining practical current-day issues, such as reintroductions, invasive species and conservation advocacy.
Last offered: Spring 2023
| Units: 1
BIO 315:
Skills to Survive and Thrive in Graduate School and Beyond
How you respond to the challenges commonly encountered in graduate school and ensuing careers impacts your motivation, productivity, health, and well-being. In this course you will learn: to recognize and rephrase negative self-talk and impostor fears; communicate more clearly and assertively with advisors; build supportive mentoring; handle (difficult) feedback; calm stress and overwhelming feelings; and boost resilience. Structure: NIH webinars and facilitated small discussion groups will provide vital individual support and help implement learned skills in daily life. This is a two-part series to be offered in both winter and spring, which progressively builds foundational well-being awareness with practical tools for sustainable impact on health and work habits.
Terms: Win, Spr
| Units: 1
| Repeatable
6 times
(up to 6 units total)
BIO 323H:
Stanford at Sea (BIO 182H, EARTHSYS 323, ESS 323, OCEANS 182H, OCEANS 323H)
(Graduate students register for 323H.) Five weeks of marine science including oceanography, marine physiology, policy, maritime studies, conservation, and nautical science at Hopkins Marine Station, followed by five weeks at sea aboard a sailing research vessel in the Pacific Ocean. Shore component comprised of three multidisciplinary courses meeting daily and continuing aboard ship. Students develop an independent research project plan while ashore, and carry out the research at sea. In collaboration with the Sea Education Association of Woods Hole, MA. Only 6 units may count towards the Biology major.
Terms: Spr
| Units: 16
BIO 332:
Evolutionary Genomics (BIO 191)
Half of the class will be reading/presenting classic and modern papers relevant to evolutionary genomics, in a "journal club" format. We will cover a broad range of topics, methods, and species. The other half will be devoted to evolutionary genomic data analysis: pairs of students will choose a data set (either their own data or published data) and a specific question, and then work throughout the quarter to answer their question.
Terms: Win
| Units: 3
BIO 342:
Plant Biology Seminar
Topics in plant biology presented at a weekly seminar. Topics announced at the beginning of each quarter. Current literature. May be repeated for credit. See https://dpb.carnegiescience.edu/events.
Last offered: Spring 2021
| Units: 1-3
| Repeatable
for credit
BIO 346:
Advanced Seminar in Microbial Molecular Biology (CSB 346, GENE 346)
Enrollment limited to PhD students associated with departmental research groups in genetics or molecular biology.
Terms: Aut, Win, Spr
| Units: 1
BIO 380:
Career Exploration and Planning
Thinking about and planning for life beyond graduate school is one of the most anxiety-provoking activities students face. In this course, students will share their personal stories and dilemmas about career decisions, discuss various career options with a PhD in life sciences, and learn to design their own path. There will be three career panels with invited guests from various career tracks, including research, teaching, administration, industry, startup, investment, law, journalism, policy, and more. Open to Biology PhD students in year 3 or beyond. The class will meet at Carnegie Institution for Science's conference room building 600, located at 260 Panama St, Stanford, CA 94305.
Last offered: Spring 2020
| Units: 1
BIO 383:
Seminar in Population Genetics
Literature review, research, and current problems in the theory and practice of population genetics and molecular evolution. May be repeated for credit. Prerequisite: consent of instructor.
Terms: Aut, Win, Spr
| Units: 1-3
| Repeatable
for credit
BIO 386:
Conservation and Population Genomics
This once a week reading and discussion group will focus on adaptive capacity: how fast and how well species, populations and individual organisms react to climate change. A rapid change in environment imposes strong changes in ecological communities. Phenotypic plasticity can change physiology or morphology, patterns of natural selection can alter gene frequencies, demographic changes can shift species ranges, changes in species interactions can change communities in species composition. This seminar will explore what we know about adaptive capacity of different communities and different species. How fast can adaptation happen? How much can adaptation `solve¿ the problems generated by climate change? How do we measure adaptive capacity? We will pull readings from the literature and structure this topic into sections. Students will present their own or published work on adaptive capacity to provide examples and frame questions. At the end, we will design an international zoom symposium to highlight, define and articulate the role that adaptive capacity can play in managing and protecting complex ecosystems in the face of climate change.
Terms: Aut, Win
| Units: 1
BIO 388:
Seminar in Computational, Evolutionary, and Human Genomics
Seminars and discussions on current topics in computational, evolutionary, and human genomics.
Terms: Aut
| Units: 2
| Repeatable
6 times
(up to 6 units total)
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.
Last offered: Spring 2020
| Units: 1
| Repeatable
for credit
BIO 802:
TGR Dissertation
Terms: Aut, Win, Spr, Sum
| Units: 0
| Repeatable
for credit
Instructors: ;
Bergmann, D. (PI);
Block, B. (PI);
Block, S. (PI);
Chen, X. (PI);
Cremer, J. (PI);
Cyert, M. (PI);
Daily, G. (PI);
Dinneny, J. (PI);
Dirzo, R. (PI);
Dixon, S. (PI);
Exposito-Alonso, M. (PI);
Feldman, J. (PI);
Feldman, M. (PI);
Field, C. (PI);
Fraser, H. (PI);
Frommer, W. (PI);
Frydman, J. (PI);
Fukami, T. (PI);
Gordon, D. (PI);
Gozani, O. (PI);
Hadly, E. (PI);
Heller, H. (PI);
Jacobs-Wagner, C. (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);
O'Connell, L. (PI);
Palumbi, S. (PI);
Peay, K. (PI);
Petrov, D. (PI);
Pritchard, J. (PI);
Red-Horse, K. (PI);
Rhee, S. (PI);
Rosenberg, N. (PI);
Sapolsky, R. (PI);
Schnitzer, M. (PI);
Schumer, M. (PI);
Shatz, C. (PI);
Shen, K. (PI);
Simon, M. (PI);
Skotheim, J. (PI);
Stearns, T. (PI);
Tessier-Lavigne, M. (PI);
Ting, A. (PI);
Tuljapurkar, S. (PI);
Vitousek, P. (PI);
Walbot, V. (PI);
Wong, W. (PI);
Turner, K. (GP)
