BIO 2N:
Ecology and Evolution of Infectious Disease in a Changing World
This seminar will explore the ways in which anthropogenic change, climate change, habitat destruction, land use change, and species invasions effects the ecology and evolution of infectious diseases. Topics will include infectious diseases of humans, wildlife, livestock, and crops, effects of disease on threatened species, disease spillover, emerging diseases, and the role of disease in natural systems. Course will be taught through a combination of popular and scientific readings, discussion, and lecture. .
Terms: Spr
| Units: 3
| UG Reqs: WAY-SMA
BIO 3:
Frontiers in Marine Biology
An introduction to contemporary research in marine biology, including ecology, conservation biology, environmental toxicology, behavior, biomechanics, evolution, neurobiology, and molecular biology. Emphasis is on new discoveries and the technologies used to make them. Weekly lectures by faculty from the Hopkins Marine Station.
Terms: Aut
| Units: 1
BIO 3N:
Views of a Changing Sea: Literature & Science
The state of a changing world ocean, particularly in the eastern Pacific, will be examined through historical and contemporary fiction, non-fiction and scientific publications. Issues will include harvest and mariculture fisheries, land-sea interactions and oceanic climate change in both surface and deep waters.
Terms: Spr
| Units: 3
| UG Reqs: GER: DB-NatSci
BIO 4N:
Peopleomics: The science and ethics of personalized genomic medicine
Exploration of the new field of personalized genomic medicine. Personalized medicine is based on the idea that each person's unique genome sequence can be used to predict risk of acquiring specific diseases, and to make more informed medical choices. The science behind these approaches; where they are heading in the future; and the ethical implications such technology presents. Lectures augmented with hands-on experience in exploring and analyzing a real person's genome.
| Units: 3
| UG Reqs: GER: DB-NatSci
BIO 7N:
Introduction to Conservation Photography
Introduction to the field of conservation photography and the strategic use of visual communication in addressing issues concerning the environment and conservation. Students will be introduced to basic digital photography, digital image processing, and the theory and application of photographic techniques. Case studies of conservation issues will be examined through photographs and multimedia platforms including images, video, and audio. Lectures, tutorials, demonstrations, and optional field trips will culminate in the production of individual and group projects.
Terms: Win
| Units: 3
| UG Reqs: WAY-CE
BIO 7SL:
Introduction to Biology Lab
Optional laboratory to be taken with BIO7S. Introduction to basic biological laboratory techniques, including microscopy, identification of biomolecules, assaying enzyme activity, genetic manipulation of microorganisms, assaying the effects of gene mutation on protein function, and using PCR to genotype organisms.
Last offered: Summer 2016
| Units: 2
BIO 8N:
Human 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.
Terms: Spr
| 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 10SC:
Natural History, Marine Biology, and Research
Monterey Bay is home to the nation¿s largest marine sanctuary and also home to Stanford's Hopkins Marine Station. This course, based at Hopkins, explores the spectacular biology of Monterey Bay and the artistic and political history of the region. We will conduct investigations across all of these contexts toward an inclusive understanding of ¿place¿, ultimately to lead us to explore our own lives in relation to the natural world, historical and cultural milieu, and the direction of our individual life path.n The location at the entry point to the Big Sur Coast of California provides a unique outdoor laboratory in which to study the biology of the bay and the adjacent coastal lands. It is also an area with a deep cultural, literary and artistic history. We will meet marine biologists, experts in the literary history of Cannery Row and the writings of John Steinbeck, local artists and photographers, experts in the neuroscience of creativity, as well as people who are very much involved in the forces and fluxes that steer modern culture. This rich and immersive approach provides students a rare opportunity to reflect on their relationships to nature, culture, and their own individual goals.nThe course emphasizes interactions and discussions. We will be together all of the time, either at our base at the Belden House in Pacific Grove, hiking and camping in Big Sur¿s pristine Big Creek Reserve on the rocky coast, and traveling to the Tassajara Mountain Zen Center in the Ventana wilderness for several days. This is not an ordinary academic experience, instead it is an adventure of a personal, intellectual, spiritual and physical kind. We welcome people with wide interests; artists, poets, writers, engineers, scientists and musicians. Mostly we invite people with an open mind and a sense of adventure. nStudents are expected to have read the several books provided as introductory material before the course begins, and each is also expected to become our local expert in an area such as plant identification, bird identification, poetry, weather prediction, photography, history, ethnography, etc. The course requires an individual research project of your choice on a topic related to the general theme. Final reports will be presented at the last meeting of the group and may involve any medium, including written, oral, and performance media.n Note: This course will be held at the Hopkins Marine Station in the Monterey region, and housing will be provided nearby. Transportation from campus to the housing site will be provided once students arrive to campus on Monday, September 4 (Labor Day). Transportation to campus from the Belden House in Pacific Grove will be provided on Saturday, September 23.
Terms: Sum
| Units: 2
BIO 12N:
Sensory Ecology of Marine Animals
Animals living in the oceans experience a highly varied range of environmental stimuli. An aquatic lifestyle requires an equally rich range of sensory adaptations, including some that are totally foreign to us. In this course we will examine sensory system in marine animals from both an environmental and behavioral perspective and from the point of view of neuroscience and information systems engineering.
Terms: Aut
| Units: 3
| UG Reqs: WAY-SMA
BIO 13Q:
Hacking the Genome
In this course, we will examine the technologies read our genetic makeup - in consumer products as well as in health and medicine - and what we can (and can't) learn about ourselves from that data. We will consider gene editing methods and their applications in health, epidemiology and agriculture, with a spotlight on the CRISPR revolution. This course will include a combination of scientific and popular literature, bioethical debates, and a short laboratory component.
Terms: Spr
| Units: 3
| UG Reqs: WAY-SMA
BIO 16:
Conservation Storytelling: Pre-course for BOSP South Africa
Limited to students admitted to the BOSP South Africa overseas seminar. Through 4 workshop meetings, students will develop and pitch story ideas, form teams in which a writer and a photographer agree to collaborate on a story, and conduct background research prior to departing for South Africa.
Last offered: Spring 2018
| Units: 1
BIO 24N:
Visions of Paradise: Garden Design
Through literature readings and field trips to local gardens learn the principles and esthetics of classic garden designs: Italian Renaissance, botanical teaching, Japanese, English cottage, and others. Design a personal vision of paradise with details of species, visual and scent impact, water features, and hardscape. Open your eyes to a new appreciation of the world of plants and learn some physiology and genetics that explains the specific properties of individual species.
Terms: Spr
| Units: 3
BIO 25Q:
Cystic fibrosis: from medical conundrum to precision medicine success story
Preference to sophomores. 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?nnThrough 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: Spr
| Units: 3
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 27S:
Evolution: From DNA to Dinosaurs
This course centers on the fundamental idea of evolution, which impacts fields as disparate as genetics to paleontology. You will learn about the history of evolutionary thought, including Darwin¿s idea of evolution by natural selection, and explore evolutionary timescales both small and large. Topics include population genetics, genomics, molecular evolution, evolutionary forces, formation of new species, evolutionary divergences in the history of life, and evidence of evolution, including patterns from DNA and the fossil record.
Terms: Sum
| Units: 3
BIO 28S:
Molecular Genetics and Biotechnology
This course covers the fundamentals of molecular genetics, including principles of how genes work, how gene expression is regulated in both prokaryotes and eukaryotes, and how signals are passed from cells to cells that are far away. We will also explore key advances in biotechnology, including cloning, sequencing, and next-generation sequencing, and discuss case studies involving cancer, Huntington¿s Disease, and more.
Terms: Sum
| Units: 3
BIO 30:
Ecology for Everyone
Everything is connected, but how? Ecology is the science of interactions and the changes they generate. This project-based course links individual behavior, population growth, species interactions, and ecosystem function. Introduction to measurement, observation, experimental design and hypothesis testing in field projects, mostly done in groups. The goal is to learn to think analytically about everyday ecological processes involving bacteria, fungi, plants, animals and humans. The course uses basic statistics to analyze data; there are no math prerequisites except arithmetic. Open to everyone, including those who may be headed for more advanced courses in ecology and environmental science.
Terms: Win
| Units: 4
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 32Q:
Neuroethology: The Neural Control of Behavior (HUMBIO 91Q)
Preference to sophomores. Animal behavior offers insights about evolutionary adaptations and this seminar will discuss the origins of the study of animal behavior and its development to the present. How does the nervous system control behavior and how is it changed by behavior? We will analyze and discuss original research papers about the neural basis of behavior. The use and misuse of parallels between animal and human behavior. Possible field trip to observe animals in their natural habitat.
Last offered: Winter 2018
| Units: 3
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 35N:
Climate change ecology: Is it too late?
This Introductory Seminar will explore the consequences of climate change on ecological communities, focusing on two emerging concepts: "disequilibrium," which emphasizes that it can take long time for communities to respond to climate change because of species interactions, and "historical contingency," which proposes that the order in which species invade and disappear as communities re-assemble in response to climate change will determine which species will persist. The seminar will involve lecture, discussion, writing, and visit to Jasper Ridge Biological Preserve.
Terms: Spr
| Units: 3
| UG Reqs: WAY-SMA
BIO 45:
Introduction to Laboratory Research in Cell and Molecular Biology
Investigate yeast strains that are engineered to express the human tumor suppressor protein, p53, and use modern molecular methods to identify the functional consequences of p53 mutations isolated from tumor cells. Learn about the protein's role as Guardian of the Genome through lectures and by reading and discussing journal articles. Use molecular visualization programs to examine the structure of normal and mutant p53 proteins. Assay the ability of mutant p53 to direct expression of several reporter genes. During guided reflection, investigate further and identify what could be wrong with the p53 mutants you have been studying. Conduct lab experiments to test hypotheses, analyze data, and present your findings through a team oral presentation, as well as a scientific poster. Although there are no pre-requisites to enroll in this class, having taken CHEM 31X, or 31A and B, and 33 and being concurrently enrolled or past enrollment in appropriate Biology Foundation classes or HumBio core classes is recommended. Note: This class has a $25 course fee.
Terms: Aut, Win
| Units: 4
| UG Reqs: WAY-SMA
BIO 46:
Introduction to Research in Ecology and Evolutionary Biology
The goal of this course is to develop an understanding of how to conduct biological research, using a topic in Ecology, Evolutionary Biology, and Plant Biology as a practical example. This includes the complete scientific process: assessing background literature, generating testable hypotheses, learning techniques for field- and lab-based data collection, analyzing data using appropriate statistical methods, and writing and sharing results. To build these skills, this course focuses on the microorganisms associated with lichen epiphytes. Students, working in teams, develop novel research hypotheses and execute the necessary experiments and measurements to test these hypotheses. In addition, students will learn how to manipulate, visualize and analyze data in R. The capstone of the course is an oral defense of students' findings, as well as a research paper in the style of a peer-reviewed journal article. Labs are completed both on campus and at Jasper Ridge. Lab fee. Information about this class is available at http://bio44.stanford.edu. Satisfies WIM in Biology.
Terms: Win
| Units: 4
| UG Reqs: WAY-SMA
BIO 47:
Introduction to Research in Ecology and Evolutionary Biology
The goal of this course is to develop an understanding of how to conduct biological research, using a topic in Ecology, Evolutionary Biology, and Plant Biology as a practical example. This includes the complete scientific process: assessing background literature, generating testable hypotheses, learning techniques for field- and lab-based data collection, analyzing data using appropriate statistical methods, and finally writing and sharing results. To build these skills, this course will focus on nectar microbes at Stanford's nearby Jasper Ridge Biological Preserve. Students, working in teams, will develop novel research hypotheses and execute the necessary experiments and measurements to test these hypotheses. The capstone of the course will be an oral defense of students' findings, as well as a research paper in the style of a peer-reviewed journal article. Labs will be completed both on campus and at Jasper Ridge. This class has a $25 course fee. Satisfies WIM in Biology.
Terms: Spr
| Units: 4
BIO 51S:
The Gene: The History and Science of our Genetic Code
This discussion-based course will use the novel ¿The gene¿ by Siddhartha Mukherjee and other selected readings to explore the science behind our genetic code. We will cover topics such as regulation of gene expression, inheritance, genetic testing, manipulation of the genome, and the relationship between genetics and identity. Prerequisites: Instructor consent, AP Biology Recommended.
Last offered: Summer 2017
| Units: 3
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.
Terms: Aut
| Units: 1
BIO 60:
Problem solving in infectious disease
Why is Lyme disease spreading? How does HIV become drug resistant? How do other animals affect our disease risk? In BIO 60 students will examine actual case studies to experience how different scientific approaches are used to battle infectious disease. They will evaluate information presented in the popular media and the scientific literature, and will directly participate in the scientific process through hands-on collection, documentation and analyses of authentic scientific data. Students will cultivate their scientific curiosity by discovering the natural world with a Foldscope, the `origami paper microscope¿ (https://microcosmos.foldscope.com). Students will build critical thinking skills by creating hypotheses, and designing experiments that pertain to problems in infectious disease. Students will work in teams to expand their thinking and will practice communicating science to different audiences.
Terms: Win
| Units: 4
| UG Reqs: WAY-SMA
BIO 61:
Science as a Creative Process (APPPHYS 61)
What is the process of science, and why does creativity matter? We'll delve deeply into the applicability of science in addressing a vast range of real-world problems. This course is designed to teach the scientific method as it's actually practiced by working scientists. It will cover how to ask a well-posed question, how to design a good experiment, how to collect and interpret quantitative data, how to recover from error, and how to communicate findings. Facts matter! Course topics will include experimental design, statistics and statistical significance, formulating appropriate controls, modeling, peer review, and more. The course will incorporate a significant hands-on component featuring device fabrication, testing, and measurement. Among other "Dorm Science" activities, we'll be distributing Arduino microcontroller kits and electronic sensors, then use these items, along with other materials, to complete a variety of group and individual projects outside the classroom. The final course assignment will be to develop and write a scientific grant proposal to test a student-selected myth or scientific controversy. Although helpful, no prior experience with electronics or computer programming is required. Recommended for freshmen.
Terms: Aut
| Units: 4
| UG Reqs: WAY-AQR, WAY-SMA
BIO 62:
Microbiology Experiments
Micro-X is an on-ramp course in which we explore classic to modern bacteriology experiments with a focus on design and logic. Bacterial biochemistry, structure, metabolism, and genetics are covered in lecture. The lab includes microbial culture, microscopic examination, and bacteriophage discovery and characterization.
Terms: Spr
| 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. 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.
Terms: Aut
| 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. Prerequisites: None.
Terms: Win
| 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.
Terms: Win
| Units: 4
| UG Reqs: WAY-SMA
BIO 85:
Evolution
Principles of evolution. Adaptation and natural selection. Darwin and the history of evolutionary thought. Population genetics, including genetic variation and mutation, and effects of migration, drift, linkage, and recombination. Evolutionary phenomena: developmental evolution, life history evolution, molecular evolution, sexual selection, social evolution, and speciation. Pattern and process in biological diversity. Case studies, including human evolution. Prerequisites: None. NOTE: Section enrollments will be handled on Canvas. Students will receive a message on how to sign up.
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 104:
Advance Molecular Biology: Epigenetics and Proteostasis (BIO 200)
Molecular mechanisms that govern the replication, recombination, and expression of eukaryotic genomes. Topics: DNA replication, DNA recombination, gene transcription, RNA splicing, regulation of gene expression, protein synthesis, and protein folding. Satisfies Central Menu Area 1. Prerequisite: Biology core or BIO 83 (BIO 82 and 86 are strongly recommended).
Terms: Win
| Units: 5
| UG Reqs: GER: DB-NatSci
BIO 105A:
Ecology and Natural History of Jasper Ridge Biological Preserve (EARTHSYS 105A)
Formerly 96A - Jasper Ridge Docent Training. First of two-quarter sequence training program to join the Jasper Ridge education/docent program. The scientific basis of ecological research in the context of a field station, hands-on field research, field ecology and the natural history of plants and animals, species interactions, archaeology, geology, hydrology, land management, multidisciplinary environmental education; and research projects, as well as management challenges of the preserve presented by faculty, local experts, and staff. Participants lead research-focused educational tours, assist with classes and research, and attend continuing education classes available to members of the JRBP community after the course.
Terms: Win
| Units: 4
BIO 105B:
Ecology and Natural History of Jasper Ridge Biological Preserve (EARTHSYS 105B)
Formerly 96B - Jasper Ridge Docent Training. Second of two-quarter sequence training program to join the Jasper Ridge education/docent program. The scientific basis of ecological research in the context of a field station, hands-on field research, field ecology and the natural history of plants and animals, species interactions, archaeology, geology, hydrology, land management, multidisciplinary environmental education; and research projects, as well as management challenges of the preserve. These topics are presented by faculty, local experts, and staff. Participants lead research-focused educational tours, assist with classes and research, and attend continuing education classes available to members of the JRBP community after the course. NOTE: All classes take place at Jasper Ridge.
Terms: Spr
| Units: 4
BIO 107:
Human Physiology Laboratory (HUMBIO 136)
This laboratory course is active and inquiry based. Aspects of exercise and temperature are explored; however, the specific questions the class tackles differ each quarter. Samples of past questions: Does lactic acid accumulation correlate with exercise fatigue at different exercise and body temperatures? Does palm cooling during exercise mitigate the effect of body temperature on fatigue with or without evaporative cooling? Students participate both as experimenters and as subjects of the experiments in two-person teams. Participants must be in good physical condition, though not necessarily athletes, and must be willing to participate in strenuous exercise routines under adverse environmental conditions. Varsity athletes concurrently participating in a spring sport must consult the instructor before applying. Discussion sessions include student presentations of journal articles, data analyses, and feedback on individual WIM research proposals. By application only, see sites.stanford.edu/bio107humbio136 for the application form. Prerequisite: Bio 84 or HumBio 4A. Satisfies WIM for Biology.nIMPORTANT NOTE: this course meets in Herrin Hall, room 202.
Terms: Spr
| Units: 4
BIO 109A:
Extending Life by Controlling Chronic Disease (BIOC 109A, BIOC 209A, HUMBIO 158)
The variability of the human genome and the role of genomic information in research, drug discovery, and human health. Concepts and interpretations of genomic markers in medical research and real life applications. Human genomes in diverse populations. Original contributions from thought leaders in academia and industry and interaction between students and guest lecturers. Students with a major, minor or coterm in Biology: 109A/209A or 109B/209B may count toward degree program but not both.
Terms: Win
| Units: 3
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 109B:
The Human Genome and Disease: Genetic Diversity and Personalized Medicine (BIOC 109B)
Continuation of 109A/209A. Genetic drift: the path of human predecessors out of Africa to Europe and then either through Asia to Australia or through northern Russia to Alaska down to the W. Coast of the Americas. Support for this idea through the histocompatibility genes and genetic sequences that predispose people to diseases. Guest lectures from academia and pharmaceutical companies. Prerequisite: Biology or Human Biology core. Students with a major, minor or coterm in Biology: 109A/209A or 109B/209B may count toward degree program but not both.
Terms: Spr
| Units: 3
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 110:
Chromatin Regulation of the Genome (BIO 210)
Maintenance of the genome is a prerequisite for life. In eukaryotes, all DNA-templated processes are tightly connected to chromatin structure and function. This course will explore epigenetic and chromatin regulation of cellular processes related to aging, cancer, stem cell pluripotency, metabolic homeostasis, and development. Course material integrates current literature with a foundational review of histone modifications and nucleosome composition in epigenetic inheritance, transcription, replication, cell division and DNA damage responses. Prerequisite: BIO 41 or BIO 83 or consent of instructor.
Terms: Spr
| Units: 3
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 112:
Human Physiology (HUMBIO 133)
Human physiology will be examined by organ systems: cardiovascular, respiratory, renal, gastrointestinal and endocrine. Molecular and cell biology and signaling principles that underlie organ development, pathophysiology and opportunities for regenerative medicine are discussed, as well as integrative control mechanisms and fetal development. Prerequisite: Human Biology core or Biology Foundations or equivalent 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. Satisfies Central Menu Areas 1 or 4. 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 115:
The Hidden Kingdom - Evolution, Ecology and Diversity of Fungi (BIO 239)
Fungi are critical, yet often hidden, components of the biosphere. They regulate decomposition, are primary partners in plant symbiosis and strongly impact agriculture and economics. Students will explore the fascinating world of fungal biology, ecology and evolution via lecture, lab, field exercises and Saturday field trips that will provide traditional and molecular experiences in the collection, analysis and industrial use of diverse fungi. Students will chose an environmental niche, collect and identify resident fungi, and hypothesize about their community relationship. Prerequisite: Bio 43 or BIO 81, 85 recommended.
Terms: Win
| Units: 4
| UG Reqs: WAY-SMA
BIO 116:
Ecology of the Hawaiian Islands (EARTHSYS 116)
Terrestrial and marine ecology and conservation biology of the Hawaiian Archipelago. Taught in the field in Hawaii as part of quarter-long sequence of courses including Earth Sciences and Anthropology. Topics include ecological succession, plant-soil interactions, conservation biology, biological invasions and ecosystem consequences, and coral reef ecology. Restricted to students accepted into the Earth Systems of Hawaii Program.
Terms: Aut
| Units: 4
| UG Reqs: GER: DB-NatSci
BIO 117:
Biology and Global Change (EARTHSYS 111, ESS 111)
The biological causes and consequences of anthropogenic and natural changes in the atmosphere, oceans, and terrestrial and freshwater ecosystems. Topics: glacial cycles and marine circulation, greenhouse gases and climate change, tropical deforestation and species extinctions, and human population growth and resource use. Prerequisite: Biology or Human Biology core or BIO 81 or graduate standing.
Terms: Win
| Units: 4
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 119:
Evolution of Marine Ecosystems (EARTHSYS 122, GEOLSCI 123, GEOLSCI 223B)
Life originally evolved in the ocean. When, why, and how did the major transitions occur in the history of marine life? What triggered the rapid evolution and diversification of animals in the Cambrian, after more than 3.5 billion years of Earth's history? What caused Earth's major mass extinction events? How do ancient extinction events compare to current threats to marine ecosystems? How has the evolution of primary producers impacted animals, and how has animal evolution impacted primary producers? In this course, we will review the latest evidence regarding these major questions in the history of marine ecosystems. We will develop familiarity with the most common groups of marine animal fossils. We will also conduct original analyses of paleontological data, developing skills both in the framing and testing of scientific hypotheses and in data analysis and presentation.
Last offered: Autumn 2017
| Units: 3-4
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 120:
Bacteria in Health and Disease (MI 120)
Enrollment limited to junior and senior undergraduates, graduate students and medical students. Introduces students to the bacteria that live in and on humans and, in some cases, can cause disease and sometimes death. Topics include the biology of the interaction of the simple microbe with complex human biology and the factors that determine whether or not we coexist relatively peacefully, suffer from overt disease, or succumb to the bacterial onslaught.
Last offered: Spring 2014
| Units: 3
BIO 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 105 or instructor approval.
Terms: Spr
| Units: 2
BIO 124:
Topics in Cancer Biology
This discussion-based course will explore the scientific tools used to study the molecular and genetic basis of cancer and to develop treatments for this disease. Topics covered may include cancer models, traditional and targeted cancer therapies, and the development of resistance to treatment. Students will develop skills in critical reading of primary research articles and will also complete a final project. Prerequisites: Biology/Human Biology core or BIO 82, 83, 86, or of instructor.
Terms: Win
| 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 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).
Terms: Spr
| Units: 4
BIO 132:
Advanced Imaging Lab in Biophysics (APPPHYS 232, BIO 232, BIOPHYS 232, GENE 232)
Laboratory and lectures. Advanced microscopy and imaging, emphasizing hands-on experience with state-of-the-art techniques. Students construct and operate working apparatus. Topics include microscope optics, Koehler illumination, contrast-generating mechanisms (bright/dark field, fluorescence, phase contrast, differential interference contrast), and resolution limits. Laboratory topics vary by year, but include single-molecule fluorescence, fluorescence resonance energy transfer, confocal microscopy, two-photon microscopy, microendoscopy, and optical trapping. Limited enrollment. Recommended: basic physics, basic cell biology, and consent of instructor.
Terms: Spr
| Units: 4
| UG Reqs: GER: DB-NatSci
BIO 133:
Network analysis for community ecology and conservation research
Graduate student led seminar. Plant-pollinator, predator-prey, and parasite-host are all examples of species interactions that can be analyzed using species interaction networks. Network analysis is an incredible tool to understand how ecological communities are impacted by environmental stressors like human development and climate change. In this class, we will review and discuss relevant scientific literature and learn how to manipulate, visualize, and interpret species interaction network data. Students will develop grant-writing skills by producing a culminating research proposal and we will take a field trip to practice species interaction sampling techniques. Prerequisites: BIO 43 or BIO 81 or BIO 85.
Terms: Spr
| Units: 2
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 RT-PCR 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 prerequisite: BIO 45, BIO 82, 83, 86.
Terms: Spr
| Units: 4
BIO 138:
Ecosystem Services: Frontiers in the Science of Valuing Nature (BIO 238, EARTHSYS 139)
This advanced course explores the science of valuing nature, beginning with its historical origins, and then its recent development in natural (especially ecological), economic, psychological, and other social sciences. We will use the ecosystem services framework (characterizing benefits from ecosystems to people) to define the state of knowledge, core methods of analysis, and research frontiers, such as at the interface with biodiversity, resilience, human health, and human development. Intended for diverse students, with a focus on research and real-world cases. To apply, please email the instructor (gdaily@stanford.edu) with a brief description of your background and research interests.
Last offered: Autumn 2017
| Units: 3
BIO 140:
The Science of Extreme Life of the Sea
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. Two lectures back to back on Tuesdays with a Writing Intermezzo between.
Terms: Spr
| 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: Aut
| 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 CHEM35 or permission of the instructor.
Terms: Aut, Spr
| Units: 3-4
| UG Reqs: WAY-SMA
BIO 144:
Conservation Biology: A Latin American Perspective (BIO 234, HUMBIO 112)
BIO 144: Conservation Biology: A Latin American Perspective (BIO 234, HUMBIO 112)nPrinciples 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. Satisfies Central Menu Area 4 for Biology majors. Prerequisite: BIO 101 or BIO 43 or HUMBIO 2A or BIO 81 and 84 or consent of instructor. 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:
Ecology and Evolution of Animal Behavior (BIO 245)
Ecological and evolutionary perspectives on animal behavior, with an emphasis on social and collective behavior. This is a project-based course in a lecture/seminar format. Seminars will be based on discussion of journal articles. Independent research projects on the behavior of animals on campus. Prerequisites: Biology or Human Biology core or BIO 81 and 85 or consent of instructor; Biology/ES 30. Recommended: statistics.
Terms: Win
| Units: 3
| UG Reqs: GER: DB-NatSci
BIO 149:
The Neurobiology of Sleep (BIO 249, HUMBIO 161)
Preference to seniors and graduate students. The neurochemistry and neurophysiology of changes in brain activity and conscious awareness associated with changes in the sleep/wake state. Behavioral and neurobiological phenomena including sleep regulation, sleep homeostasis, circadian rhythms, sleep disorders, sleep function, and the molecular biology of sleep. Enrollment limited to 16.
Terms: Win
| Units: 4
| UG Reqs: GER: DB-NatSci
BIO 150:
Human Behavioral Biology (HUMBIO 160)
Multidisciplinary. How to approach complex normal and abnormal behaviors through biology. How to integrate disciplines including sociobiology, ethology, neuroscience, and endocrinology to examine behaviors such as aggression, sexual behavior, language use, and mental illness.
Last offered: Spring 2018
| Units: 5
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 151:
Mechanisms of Neuron Death
For Biology majors with background in neuroscience. Cell and molecular biology of neuron death during neurological disease. Topics: the amyloid diseases (Alzheimer's), prion diseases (kuru and Creutzfeldt-Jakob), oxygen radical diseases (Parkinson's and ALS), triplet repeat diseases (Huntington's), and AIDS-related dementia. Student presentations. Enrollment limited to 15; application required.
Terms: Aut
| Units: 3
| UG Reqs: GER: DB-NatSci
BIO 152:
Imaging: Biological Light Microscopy (CSB 222, MCP 222)
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, Win
| Units: 3
| UG Reqs: GER: DB-NatSci
BIO 153:
Cellular Neuroscience: Cell Signaling and Behavior (PSYCH 120)
Neural interactions underlying behavior. Prerequisites: PSYCH 1 or basic biology.
Terms: Aut
| Units: 4
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 154:
Molecular and Cellular Neurobiology
For advanced undergraduate students. Cellular and molecular mechanisms in the organization and functions of the nervous system. Topics: wiring of the neuronal circuit, synapse structure and synaptic transmission, signal transduction in the nervous system, sensory systems, molecular basis of behavior including learning and memory, molecular pathogenesis of neurological diseases. Satisfies Central Menu Areas 2 or 3 for Bio majors. Highly recommended: BioCore or BIO 82, 83, 86, or consent of instructor.
Terms: Win
| Units: 4
| UG Reqs: GER: DB-NatSci
BIO 157:
Biochemistry and Molecular Biology of Plants
Biochemical and molecular basis of plant growth and adaptation. Topics include: hormone signal transduction; photoreceptor chemistry and signaling; metabolite sensing and transport; dynamics of photosynthesis; plant innate immunity and symbiosis. Lectures and readings will emphasize research methods. Prerequisite: Biology core or equivalent, or consent of instructor.
Last offered: Spring 2014
| Units: 3-4
| UG Reqs: GER: DB-NatSci
BIO 158:
Developmental Neurobiology (BIO 258)
For advanced undergraduates and coterminal students. The principles of nervous system development from the molecular control of patterning, cell-cell interactions, and trophic factors to the level of neural systems and the role of experience in influencing brain structure and function. Topics: neural induction and patterning cell lineage, neurogenesis, neuronal migration, axonal pathfinding, synapse elimination, the role of activity, critical periods, and the development of behavior. Satisfies Central Menu Areas 2 or 3. Prerequisite: BIO 42 or BIO 82, 83, 84, 86.
Terms: Aut
| Units: 4
| UG Reqs: GER: DB-NatSci, WAY-SMA
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 167:
Insulin and carbohydrate metabolism in health and disease a history of advances 1850 to current
The quest to understand how the body uses sugar and the overlapping quest for a diabetes cure have resulted in discoveries in every branch of biology. Topics include insulin production, structure, and evolution; transduction of the insulin signal; transport of sugar into cells; sugar storage and release; how the brain transports and uses sugar; growth control; pancreas development; genetic and environmental causes of diabetes; engineering solutions to diabetes (artificial pancreas, stem cells), glucose homeostasis (modeling insulin action). Prerequisites: BIO 41, 42.
Terms: Spr
| Units: 3
BIO 168:
Explorations in Stem Cell Biology
A discussion-based course for advanced undergraduates. The purpose of this course is to introduce students to key topics in stem cell biology and foster the development of strong scientific writing skills. We will review and discuss some landmark and current primary literature in the stem cell field. Topics will include embryonic and adult stem cells, cellular reprogramming and stem cells in disease and regenerative medicine. Students will present a current research paper in their preferred stem cell topic area and compose a novel research proposal. Prerequisites: Biology or Human Biology core or BIO 82, 83, 86. Satisfies WIM in Biology.
Terms: Aut
| Units: 3
BIO 171:
Principles of Cell Cycle Control (BIO 271, CSB 271)
Genetic analysis of the key regulatory circuits governing the control of cell division. Illustration of key principles that can be generalized to other synthetic and natural biological circuits. Focus on tractable model organisms; growth control; irreversible biochemical switches; chromosome duplication; mitosis; DNA damage checkpoints; MAPK pathway-cell cycle interface; oncogenesis. Analysis of classic and current primary literature. Satisfies Central Menu Area 2.
Terms: Aut
| Units: 3
| UG Reqs: GER: DB-NatSci
BIO 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 174:
Human Skeletal Anatomy (ANTHRO 175, ANTHRO 275, BIO 274, HUMBIO 180)
Study of the human skeleton (a. k. a. human osteology), as it bears on other disciplines, including medicine, forensics, archaeology, and paleoanthropology (human evolution). Basic bone biology, anatomy, and development, emphasizing hands-on examination and identification of human skeletal parts, their implications for determining an individual¿s age, sex, geographic origin, and health status, and for the evolutionary history of our species. Three hours of lecture and at least three hours of supervised and independent study in the lab each week.
Terms: Win
| Units: 5
| UG Reqs: GER: DB-NatSci, WAY-SMA
BIO 175:
Collective Behavior and Distributed Intelligence (SYMSYS 275)
This course will explore possibilities for student research projects based on presentations of faculty research. We will cover a broad range of topics within the general area of collective behavior, both natural and artificial. Students will build on faculty presentations to develop proposals for future projects.
Last offered: Spring 2018
| Units: 3
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.
Terms: Win
| Units: 4
BIO 177:
Plant Microbe Interaction (BIO 277)
Molecular basis of plant symbiosis and pathogenesis. Topics include mechanisms of recognition and signaling between microbes and plant hosts, with examples such as the role of small molecules, secreted peptides, and signal transduction pathways in symbiotic or pathogenic interactions. Readings include landmark papers together with readings in the contemporary literature. Prerequisites: Biology core and two or more upper division courses in genetics, molecular biology, or biochemistry. Recommended: plant genetics or plant biochemistry.
Terms: Spr
| Units: 3
BIO 178:
Microbiology Literature (BIO 278)
For advanced undergraduates and first-year graduate students. Critical reading of the research literature in prokaryotic genetics and molecular biology, with particular applications to the study of major human pathogens. Classic and foundational papers in pathogenesis, genetics, and molecular biology; recent literature on bacterial pathogens such as Salmonella, Vibrio, and/or Yersinia. Diverse experimental approaches: biochemistry, genomics, pathogenesis, and cell biology. Prerequisites: Biology Core and two upper-division courses in genetics, molecular biology, or biochemistry.
Last offered: Winter 2018
| Units: 3
BIO 180:
Microbial Physiology (EARTHSYS 255, ESS 255, 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.
Terms: Win
| Units: 3
BIO 182:
Modeling Cultural Evolution (BIO 282)
Seminar. Quantitative models for the evolution of socially transmitted traits. Rates of change of learned traits in populations and patterns of cultural diversity as a function of innovation and cultural transmission. Learning in constant and changing environments. Possible avenues for gene-culture coevolution.
Terms: Win
| Units: 3
BIO 183:
Theoretical Population Genetics (BIO 283)
Models in population genetics and evolution. Selection, random drift, gene linkage, migration, and inbreeding, and their influence on the evolution of gene frequencies and chromosome structure. Models are related to DNA sequence evolution. Prerequisites: calculus and linear algebra, or consent of instructor.
Last offered: Winter 2018
| Units: 3
| UG Reqs: WAY-AQR, WAY-SMA
BIO 193:
Interdisciplinary Approaches to Human Health Research (BIOE 193, CHEM 113, 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.
Terms: Win, Spr
| 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
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.
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
Terms: Spr
| Units: 3
| UG Reqs: WAY-CE
| Repeatable
2 times
(up to 6 units total)
BIO 197WA:
Senior Writing Project: The Personal Essay in Biology
Seminar focused on writing. Compose, workshop and revise scientifically relevant and personal essays in biology directed at a mainstream audience, interweaving research, interview, memoir, and other elements of nonfiction craft. Satisfies WIM in Biology.
Terms: Win, Spr
| Units: 3
BIO 198:
Directed Reading in Biology
Individually arranged under the supervision of members of the faculty.
Terms: Aut, Win, Spr, Sum
| Units: 1-15
| Repeatable
10 times
(up to 60 units total)
Instructors: ;
Barton, K. (PI);
Bergmann, D. (PI);
Berry, J. (PI);
Block, B. (PI);
Block, S. (PI);
Boggs, C. (PI);
Chen, X. (PI);
Crowder, L. (PI);
Cyert, M. (PI);
Daily, G. (PI);
Denny, M. (PI);
Dinneny, J. (PI);
Dirzo, R. (PI);
Dixon, S. (PI);
Ehrlich, P. (PI);
Epel, D. (PI);
Feldman, J. (PI);
Feldman, M. (PI);
Fernald, R. (PI);
Field, C. (PI);
Fraser, H. (PI);
Frommer, W. (PI);
Frydman, J. (PI);
Fukami, T. (PI);
Gilly, W. (PI);
Goldbogen, J. (PI);
Gordon, D. (PI);
Gozani, O. (PI);
Grossman, A. (PI);
Hadly, E. (PI);
Hanawalt, P. (PI);
Heller, H. (PI);
Jones, P. (PI);
Khalfan, W. (PI);
Klein, R. (PI);
Kopito, R. (PI);
Long, S. (PI);
Lowe, C. (PI);
Luo, L. (PI);
McConnell, S. (PI);
Micheli, F. (PI);
Mooney, H. (PI);
Mordecai, E. (PI);
Morrison, A. (PI);
Mudgett, M. (PI);
Nelson, W. (PI);
O'Connell, L. (PI);
Palumbi, S. (PI);
Peay, K. (PI);
Petrov, D. (PI);
Pritchard, J. (PI);
Red-Horse, K. (PI);
Rosenberg, N. (PI);
Roughgarden, J. (PI);
Sapolsky, R. (PI);
Schnitzer, M. (PI);
Seawell, P. (PI);
Shatz, C. (PI);
Shen, K. (PI);
Simon, M. (PI);
Simoni, R. (PI);
Skotheim, J. (PI);
Somero, G. (PI);
Spormann, A. (PI);
Stearns, T. (PI);
Tessier-Lavigne, M. (PI);
Thompson, S. (PI);
Ting, A. (PI);
Todhunter, A. (PI);
Tuljapurkar, S. (PI);
Vitousek, P. (PI);
Walbot, V. (PI);
Wang, Z. (PI);
Watt, W. (PI)
BIO 198X:
Out-of-Department Directed Reading
Individually arranged under the supervision of members of the faculty. Credit for work arranged with out-of-department faculty is restricted to Biology majors and requires department approval. See https://biology.stanford.edu/academics/undergraduate-research/directed-reading for information and petitions. May be repeated for credit.
Terms: Aut, Win, Spr, Sum
| Units: 1-15
| Repeatable
10 times
(up to 60 units total)
Instructors: ;
Bergmann, D. (PI);
Block, B. (PI);
Block, S. (PI);
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);
Frommer, W. (PI);
Frydman, J. (PI);
Fukami, T. (PI);
Gilly, W. (PI);
Gordon, D. (PI);
Gozani, O. (PI);
Hadly, E. (PI);
Hanawalt, P. (PI);
Heller, H. (PI);
Jones, P. (PI);
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);
Skotheim, J. (PI);
Somero, G. (PI);
Stearns, T. (PI);
Thompson, S. (PI);
Tuljapurkar, S. (PI);
Vitousek, P. (PI);
Walbot, V. (PI)
BIO 199:
Advanced Research Laboratory in Experimental Biology
Individual research taken by arrangement with in-department instructors. See http://biohonors.stanford.edu for information on research sponsors, units, and credit for summer research. May be repeated for credit.
Terms: Aut, Win, Spr, Sum
| Units: 1-15
| Repeatable
15 times
(up to 60 units total)
Instructors: ;
Barton, K. (PI);
Bergmann, D. (PI);
Berry, J. (PI);
Block, B. (PI);
Block, S. (PI);
Boggs, C. (PI);
Chen, X. (PI);
Crowder, L. (PI);
Cyert, M. (PI);
Daily, G. (PI);
Denny, M. (PI);
Dinneny, J. (PI);
Dirzo, R. (PI);
Dixon, S. (PI);
Ehrlich, P. (PI);
Epel, D. (PI);
Feldman, J. (PI);
Feldman, M. (PI);
Fernald, R. (PI);
Field, C. (PI);
Fraser, H. (PI);
Frommer, W. (PI);
Frydman, J. (PI);
Fukami, T. (PI);
Gilly, W. (PI);
Gordon, D. (PI);
Gozani, O. (PI);
Grossman, A. (PI);
Hadly, E. (PI);
Hanawalt, P. (PI);
Heller, H. (PI);
Jones, P. (PI);
Klein, R. (PI);
Kopito, R. (PI);
Long, S. (PI);
Lowe, C. (PI);
Luo, L. (PI);
McConnell, S. (PI);
Micheli, F. (PI);
Mooney, H. (PI);
Mordecai, E. (PI);
Morrison, A. (PI);
Mudgett, M. (PI);
Nelson, W. (PI);
O'Connell, L. (PI);
Palumbi, S. (PI);
Peay, K. (PI);
Petrov, D. (PI);
Pritchard, J. (PI);
Red-Horse, K. (PI);
Rosenberg, N. (PI);
Roughgarden, J. (PI);
Sapolsky, R. (PI);
Schnitzer, M. (PI);
Shatz, C. (PI);
Shen, K. (PI);
Simon, M. (PI);
Simoni, R. (PI);
Skotheim, J. (PI);
Somero, G. (PI);
Stearns, T. (PI);
Tessier-Lavigne, M. (PI);
Thompson, S. (PI);
Ting, A. (PI);
Tuljapurkar, S. (PI);
Vitousek, P. (PI);
Walbot, V. (PI);
Wang, Z. (PI);
Watt, W. (PI)
BIO 199W:
Senior Honors Thesis: How to Effectively Write About Scientific Research
Workshop. For seniors pursuing an honors thesis in a biology-focused major or program. Focus on improving scientific writing and synthesizing in the context of students' individual research projects. Complete literature review which will form the basis for the thesis introduction. Develop methods section of the thesis. Small seminar-style discussion sections with research-based discussions, student led PowerPoint presentations, and writing workshops. Co-requisite: Concurrent enrollment in 199 or 199X or equivalent. Satisfies WIM in Biology.
Terms: Win
| Units: 3
BIO 199X:
Out-of-Department Advanced Research Laboratory in Experimental Biology
Individual research by arrangement with out-of-department instructors. Credit for 199X is restricted to declared Biology majors and requires department approval. See https://biology.stanford.edu/academics/undergraduate-research/research for information on research sponsors, units, petitions, deadlines, credit for summer research, and out-of-Stanford research. May be repeated for credit.
Terms: Aut, Win, Spr, Sum
| Units: 1-15
| Repeatable
15 times
(up to 60 units total)
Instructors: ;
Barres, B. (PI);
Beachy, P. (PI);
Bergmann, D. (PI);
Bertozzi, C. (PI);
Bhalla, V. (PI);
Bhutani, N. (PI);
Blau, H. (PI);
Blish, C. (PI);
Block, B. (PI);
Block, S. (PI);
Brunet, A. (PI);
Chang, H. (PI);
Chen, L. (PI);
Cheng, A. (PI);
Clandinin, T. (PI);
Crowder, L. (PI);
Cui, B. (PI);
Cyert, M. (PI);
Daily, G. (PI);
Davis, M. (PI);
Deisseroth, K. (PI);
Denny, M. (PI);
Dirzo, R. (PI);
Dixon, S. (PI);
Ebel, E. (PI);
Egan, E. (PI);
Ehrlich, P. (PI);
Feldman, M. (PI);
Felsher, D. (PI);
Fernald, R. (PI);
Field, C. (PI);
Fraser, H. (PI);
Frydman, J. (PI);
Fuller, M. (PI);
Garcia, C. (PI);
Gilly, W. (PI);
Gordon, D. (PI);
Gozani, O. (PI);
Graves, E. (PI);
Gurtner, G. (PI);
Hadly, E. (PI);
Hallmayer, J. (PI);
Hanawalt, P. (PI);
Heller, H. (PI);
Heller, S. (PI);
Jeffrey, S. (PI);
Jones, P. (PI);
Khavari, P. (PI);
Kim, P. (PI);
Kim, S. (PI);
Knutson, B. (PI);
Kopito, R. (PI);
Kuo, C. (PI);
Levitt, M. (PI);
Long, J. (PI);
Long, S. (PI);
Longaker, M. (PI);
Lowe, C. (PI);
Luo, L. (PI);
MacIver, M. (PI);
Madison, D. (PI);
Martinez, O. (PI);
McConnell, S. (PI);
Micheli, F. (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);
O'Brien, L. (PI);
Oro, A. (PI);
Palmer, T. (PI);
Palumbi, S. (PI);
Petrov, D. (PI);
Pitteri, S. (PI);
Plant, G. (PI);
Pollack, J. (PI);
Porteus, M. (PI);
Prince, D. (PI);
Puglisi, J. (PI);
Quertermous, T. (PI);
Raymond, J. (PI);
Red-Horse, K. (PI);
Relman, D. (PI);
Sapolsky, R. (PI);
Schnitzer, M. (PI);
Shamloo, M. (PI);
Shatz, C. (PI);
Shen, K. (PI);
Simon, M. (PI);
Skotheim, J. (PI);
Stearns, T. (PI);
Steinberg, G. (PI);
Stevenson, D. (PI);
Stoyanova, T. (PI);
Straight, A. (PI);
Sudhof, T. (PI);
Thompson, S. (PI);
Ting, A. (PI);
Tuljapurkar, S. (PI);
Utz, P. (PI);
Vitousek, P. (PI);
Walbot, V. (PI);
Wang, K. (PI);
Weissman, I. (PI);
Wu, J. (PI);
Wyss-Coray, T. (PI);
Zhao, H. (PI);
Johnson, S. (GP);
Nogoy, C. (GP);
O'Neal, A. (GP);
Stearns, T. (GP)
BIO 200:
Advance Molecular Biology: Epigenetics and Proteostasis (BIO 104)
Molecular mechanisms that govern the replication, recombination, and expression of eukaryotic genomes. Topics: DNA replication, DNA recombination, gene transcription, RNA splicing, regulation of gene expression, protein synthesis, and protein folding. Satisfies Central Menu Area 1. Prerequisite: Biology core or BIO 83 (BIO 82 and 86 are strongly recommended).
Terms: Win
| Units: 5
BIO 202:
Ecological Statistics
Intended for graduate students (and advanced undergraduates in special circumstances with consent of instructors) in biology and related environmental sciences, this course is an introduction to statistical methods for ecological data analysis, using the programming language R. The course will have lectures, discussions, and independent research projects using the students' own data or simulated or publicly available data.
Last offered: Autumn 2017
| Units: 3
BIO 204:
Neuroplasticity: From Synapses to Behavior
This course will focus on neuroplasticity from a broad perspective, from molecular cellular mechanism to its involvement in behavior and diseases. Emphasis will be on: a) molecular and cellular mechanisms underlying various forms of neuroplasticity; b) the neuroplasticity during brain development; c) the neuroplasticity in adult brain with respect to learning and memory; and d) maladaptive neuroplasticity in neurodegenerative disease and drug addiction. This course is designed for Ph.D. students from both the Biology and Neuroscience programs. Open to advanced undergraduates by consent of instructor.
Terms: Spr
| Units: 3
BIO 208:
Spanish in Science/Science in Spanish (EARTHSYS 207, LATINAM 207)
For graduate and undergraduate students interested in the natural sciences and the Spanish language. Students will acquire the ability to communicate in Spanish using scientific language and will enhance their ability to read scientific literature written in Spanish. Emphasis on the development of science in Spanish-speaking countries or regions. Course is conducted in Spanish and intended for students pursuing degrees in the sciences, particularly disciplines such as ecology, environmental science, sustainability, resource management, anthropology, and archeology.
Terms: Spr
| Units: 2
| Repeatable
2 times
(up to 4 units total)
BIO 210:
Chromatin Regulation of the Genome (BIO 110)
Maintenance of the genome is a prerequisite for life. In eukaryotes, all DNA-templated processes are tightly connected to chromatin structure and function. This course will explore epigenetic and chromatin regulation of cellular processes related to aging, cancer, stem cell pluripotency, metabolic homeostasis, and development. Course material integrates current literature with a foundational review of histone modifications and nucleosome composition in epigenetic inheritance, transcription, replication, cell division and DNA damage responses. Prerequisite: BIO 41 or BIO 83 or consent of instructor.
Terms: Spr
| Units: 3
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. Preparation of an original research proposal. Prerequisite for advanced undergraduates: BIO 129A or 160, and consent of instructor.
Terms: Win
| Units: 4
Instructors: ;
Brandman, O. (PI);
Ehrhardt, D. (PI);
Ferrell, J. (PI);
Kopito, R. (PI);
Li, L. (PI);
Pfeffer, S. (PI);
Rohatgi, R. (PI);
Spudich, J. (PI);
Ting, A. (PI);
Kirkegaard, K. (SI);
Lu Lopez, A. (SI)
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 105 or instructor approval.
Terms: Spr
| Units: 2
BIO 222:
Exploring Neural Circuits
Seminar. The logic of how neural circuits control behavior; how neural circuits are assembled during development and modified by experience. Emphasis is on primary literature. Topics include: neurons as information processing units; simple and complex circuits underlying sensory information processing and motor control; and development and plasticity of neural circuits. Advanced undergraduates and graduate students with background in physical science, engineering, and biology may apply to enroll. Enrollment is by application only. Recommended: background in neuroscience.
Terms: Spr
| Units: 3
BIO 223:
Stochastic and Nonlinear Dynamics (APPPHYS 223, BIOE 213, 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: Spr
| Units: 3
BIO 226:
Introduction to Biophysics (APPPHYS 205, BIO 126)
Core course appropriate for advanced undergraduate students and graduate students with prior knowledge of calculus and a college physics course. Introduction to how physical principles offer insights into modern biology, with regard to the structural, dynamical, and functional organization of biological systems. Topics include the roles of free energy, diffusion, electromotive forces, non-equilibrium dynamics, and information in fundamental biological processes.
Terms: Win
| Units: 3-4
BIO 227:
Foundations of Community Ecology
Discussion of classic papers in community ecology (Forbes, Clements, Gleason, Grinnell, Lindeman, Preston, Elton, Hutchinson, May, MacArthur, Odum, Connell, Paine, Tilman, etc.) and contemporary papers on related topics, to develop historical perspectives to understand current issues and identify future directions. Prerequisite for undergraduates: consent of instructor.
Terms: Aut
| Units: 2
BIO 230:
Molecular and Cellular Immunology
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 of immune responses and their regulation; genetic control of immune responses and disease susceptibility; immunotherapies for treating diseases. Lectures and discussion in class and in sections. Satisfies Central Menu Areas 1 or 2. 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 230A:
Molecular and Cellular Immunology Literature Review
Special discussion section for graduate students. Supplement to BIO 230. Pre- or corequisite: BIO 230 or other introductory immunology course.
Terms: Aut
| Units: 1
BIO 232:
Advanced Imaging Lab in Biophysics (APPPHYS 232, BIO 132, BIOPHYS 232, GENE 232)
Laboratory and lectures. Advanced microscopy and imaging, emphasizing hands-on experience with state-of-the-art techniques. Students construct and operate working apparatus. Topics include microscope optics, Koehler illumination, contrast-generating mechanisms (bright/dark field, fluorescence, phase contrast, differential interference contrast), and resolution limits. Laboratory topics vary by year, but include single-molecule fluorescence, fluorescence resonance energy transfer, confocal microscopy, two-photon microscopy, microendoscopy, and optical trapping. Limited enrollment. Recommended: basic physics, basic cell biology, and consent of instructor.
Terms: Spr
| Units: 4
BIO 234:
Conservation Biology: A Latin American Perspective (BIO 144, HUMBIO 112)
BIO 144: Conservation Biology: A Latin American Perspective (BIO 234, HUMBIO 112)nPrinciples 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. Satisfies Central Menu Area 4 for Biology majors. Prerequisite: BIO 101 or BIO 43 or HUMBIO 2A or BIO 81 and 84 or consent of instructor. 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 238:
Ecosystem Services: Frontiers in the Science of Valuing Nature (BIO 138, EARTHSYS 139)
This advanced course explores the science of valuing nature, beginning with its historical origins, and then its recent development in natural (especially ecological), economic, psychological, and other social sciences. We will use the ecosystem services framework (characterizing benefits from ecosystems to people) to define the state of knowledge, core methods of analysis, and research frontiers, such as at the interface with biodiversity, resilience, human health, and human development. Intended for diverse students, with a focus on research and real-world cases. To apply, please email the instructor (gdaily@stanford.edu) with a brief description of your background and research interests.
Last offered: Autumn 2017
| Units: 3
BIO 239:
The Hidden Kingdom - Evolution, Ecology and Diversity of Fungi (BIO 115)
Fungi are critical, yet often hidden, components of the biosphere. They regulate decomposition, are primary partners in plant symbiosis and strongly impact agriculture and economics. Students will explore the fascinating world of fungal biology, ecology and evolution via lecture, lab, field exercises and Saturday field trips that will provide traditional and molecular experiences in the collection, analysis and industrial use of diverse fungi. Students will chose an environmental niche, collect and identify resident fungi, and hypothesize about their community relationship. Prerequisite: Bio 43 or BIO 81, 85 recommended.
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. Satisfies Central Menu Areas 1 or 4. Prerequisites: Biology core or BIO 82, 85 or graduate standing in any department, and consent of instructor.
Terms: Win
| Units: 4
BIO 245:
Ecology and Evolution of Animal Behavior (BIO 145)
Ecological and evolutionary perspectives on animal behavior, with an emphasis on social and collective behavior. This is a project-based course in a lecture/seminar format. Seminars will be based on discussion of journal articles. Independent research projects on the behavior of animals on campus. Prerequisites: Biology or Human Biology core or BIO 81 and 85 or consent of instructor; Biology/ES 30. Recommended: statistics.
Terms: Win
| Units: 3
BIO 247:
Genomic approaches to the study of human disease (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: Aut
| Units: 3
BIO 249:
The Neurobiology of Sleep (BIO 149, HUMBIO 161)
Preference to seniors and graduate students. The neurochemistry and neurophysiology of changes in brain activity and conscious awareness associated with changes in the sleep/wake state. Behavioral and neurobiological phenomena including sleep regulation, sleep homeostasis, circadian rhythms, sleep disorders, sleep function, and the molecular biology of sleep. Enrollment limited to 16.
Terms: Win
| Units: 4
BIO 251:
Evolution by the numbers (APPPHYS 237)
Topics in evolution from a quantitative perspective. From basic principles of evolutionary dynamics to fundamental questions that are far-from-being answered; from early life, metabolic processes, and the molding of the earth by microbes, to spread of human epidemics; from analysis of genomes and molecular phylogenies to aspects of multi-cellular development. Intended for students with no biology background as well as biology students who are comfortable with probability and ordinary differential equations. Advanced undergraduate as well.
Terms: Aut
| Units: 3
BIO 254:
Molecular and Cellular Neurobiology (NBIO 254)
For graduate students. Includes lectures for BIO 154. Cellular and molecular mechanisms in the organization and functions of the nervous system. Topics: wiring of the neuronal circuit, synapse structure and synaptic transmission, signal transduction in the nervous system, sensory systems, molecular basis of behavior including learning and memory, molecular pathogenesis of neurological diseases.
Terms: Win
| Units: 3-5
BIO 258:
Developmental Neurobiology (BIO 158)
For advanced undergraduates and coterminal students. The principles of nervous system development from the molecular control of patterning, cell-cell interactions, and trophic factors to the level of neural systems and the role of experience in influencing brain structure and function. Topics: neural induction and patterning cell lineage, neurogenesis, neuronal migration, axonal pathfinding, synapse elimination, the role of activity, critical periods, and the development of behavior. Satisfies Central Menu Areas 2 or 3. Prerequisite: BIO 42 or BIO 82, 83, 84, 86.
Terms: Aut
| Units: 4
BIO 267:
Molecular Mechanisms of Neurodegenerative Disease (GENE 267, NENS 267)
The epidemic of neurodegenerative disorders such as Alzheimer's and Parkinson's disease occasioned by an aging human population. Genetic, molecular, and cellular mechanisms. Clinical aspects through case presentations.nnThis 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 2018
| Units: 4
BIO 268:
Statistical and Machine Learning Methods for Genomics (BIOMEDIN 245, CS 373, GENE 245, STATS 345)
Introduction to statistical and computational methods for genomics. Sample topics include: expectation maximization, hidden Markov model, Markov chain Monte Carlo, ensemble learning, probabilistic graphical models, kernel methods and other modern machine learning paradigms. Rationales and techniques illustrated with existing implementations used in population genetics, disease association, and functional regulatory genomics studies. Instruction includes lectures and discussion of readings from primary literature. Homework and projects require implementing some of the algorithms and using existing toolkits for analysis of genomic datasets.
Last offered: Spring 2018
| Units: 3
BIO 271:
Principles of Cell Cycle Control (BIO 171, CSB 271)
Genetic analysis of the key regulatory circuits governing the control of cell division. Illustration of key principles that can be generalized to other synthetic and natural biological circuits. Focus on tractable model organisms; growth control; irreversible biochemical switches; chromosome duplication; mitosis; DNA damage checkpoints; MAPK pathway-cell cycle interface; oncogenesis. Analysis of classic and current primary literature. Satisfies Central Menu Area 2.
Terms: Aut
| Units: 3
| UG Reqs: GER: DB-NatSci
BIO 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, 35, and BIOSCI 41, CHEMENG 181 (formerly 188), or equivalents.
Terms: Win
| 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.
| Units: 3
BIO 274:
Human Skeletal Anatomy (ANTHRO 175, ANTHRO 275, BIO 174, HUMBIO 180)
Study of the human skeleton (a. k. a. human osteology), as it bears on other disciplines, including medicine, forensics, archaeology, and paleoanthropology (human evolution). Basic bone biology, anatomy, and development, emphasizing hands-on examination and identification of human skeletal parts, their implications for determining an individual¿s age, sex, geographic origin, and health status, and for the evolutionary history of our species. Three hours of lecture and at least three hours of supervised and independent study in the lab each week.
Terms: Win
| Units: 5
BIO 274S:
Hopkins Microbiology Course (BIOHOPK 274, CEE 274S, ESS 253S)
(Formerly GES 274S.) Four-week, intensive. The interplay between molecular, physiological, ecological, evolutionary, and geochemical processes that constitute, cause, and maintain microbial diversity. How to isolate key microorganisms driving marine biological and geochemical diversity, interpret culture-independent molecular characterization of microbial species, and predict causes and consequences. Laboratory component: what constitutes physiological and metabolic microbial diversity; how evolutionary and ecological processes diversify individual cells into physiologically heterogeneous populations; and the principles of interactions between individuals, their population, and other biological entities in a dynamically changing microbial ecosystem. Prerequisites: CEE 274A and CEE 274B, or equivalents.
Terms: Sum
| Units: 3-12
| Repeatable
for credit
BIO 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.
Terms: Win
| Units: 4
BIO 277:
Plant Microbe Interaction (BIO 177)
Molecular basis of plant symbiosis and pathogenesis. Topics include mechanisms of recognition and signaling between microbes and plant hosts, with examples such as the role of small molecules, secreted peptides, and signal transduction pathways in symbiotic or pathogenic interactions. Readings include landmark papers together with readings in the contemporary literature. Prerequisites: Biology core and two or more upper division courses in genetics, molecular biology, or biochemistry. Recommended: plant genetics or plant biochemistry.
Terms: Spr
| Units: 3
BIO 278:
Microbiology Literature (BIO 178)
For advanced undergraduates and first-year graduate students. Critical reading of the research literature in prokaryotic genetics and molecular biology, with particular applications to the study of major human pathogens. Classic and foundational papers in pathogenesis, genetics, and molecular biology; recent literature on bacterial pathogens such as Salmonella, Vibrio, and/or Yersinia. Diverse experimental approaches: biochemistry, genomics, pathogenesis, and cell biology. Prerequisites: Biology Core and two upper-division courses in genetics, molecular biology, or biochemistry.
Last offered: Winter 2018
| Units: 3
BIO 279:
Integrated Valuation of Ecosystem Services and Tradeoffs
This course explores the science of valuing nature, with a brief overview of its historical origins and then a primary focus on its recent development in the sciences (ecology, hydrology, and health sciences, integrating some economics, psychology, and other social sciences). The principal aim of the course is to enable facility in new research and real-world applications of InVEST models (for integrated valuation of ecosystem services and tradeoffs). Prerequisite: some experience with GIS (geographic information systems). Permission from the instructor is required. (Email Prof. Daily gdaily@stanford.edu.)
Terms: Win
| 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 2018
| Units: 3
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: Win
| Units: 3
BIO 290:
Teaching of Biology
Open to upper-division undergraduates and graduate students. Practical experience in teaching lab biology or serving as an assistant in a lecture course. May be repeated for credit. Prerequisite: consent of instructor.
Terms: Aut, Win, Spr, Sum
| Units: 1-5
| Repeatable
for credit
Instructors: ;
Barton, K. (PI);
Bergmann, D. (PI);
Berry, J. (PI);
Block, B. (PI);
Block, S. (PI);
Boggs, C. (PI);
Chen, X. (PI);
Crowder, L. (PI);
Cyert, M. (PI);
Daily, G. (PI);
Denny, M. (PI);
Dirzo, R. (PI);
Dixon, S. (PI);
Ehrlich, P. (PI);
Endy, D. (PI);
Feldman, J. (PI);
Feldman, M. (PI);
Fernald, R. (PI);
Field, C. (PI);
Fraser, H. (PI);
Frommer, W. (PI);
Frydman, J. (PI);
Fukami, T. (PI);
Gilly, W. (PI);
Goldbogen, J. (PI);
Gordon, D. (PI);
Gozani, O. (PI);
Greco, R. (PI);
Grossman, A. (PI);
Hadly, E. (PI);
Hanawalt, P. (PI);
Hekmat-Scafe, D. (PI);
Heller, H. (PI);
Heller, R. (PI);
Imam, J. (PI);
Jones, P. (PI);
Khalfan, W. (PI);
Klein, R. (PI);
Knope, M. (PI);
Kopito, R. (PI);
Long, S. (PI);
Lowe, C. (PI);
Luo, L. (PI);
Malladi, S. (PI);
McConnell, S. (PI);
Micheli, F. (PI);
Mooney, H. (PI);
Mordecai, E. (PI);
Morrison, A. (PI);
Mudgett, M. (PI);
Nelson, W. (PI);
Palumbi, S. (PI);
Petrov, D. (PI);
Red-Horse, K. (PI);
Rosenberg, N. (PI);
Sapolsky, R. (PI);
Schnitzer, M. (PI);
Seawell, P. (PI);
Shatz, C. (PI);
Shen, K. (PI);
Simon, M. (PI);
Simoni, R. (PI);
Skotheim, J. (PI);
Somero, G. (PI);
Stearns, T. (PI);
Thompson, S. (PI);
Tuljapurkar, S. (PI);
Vitousek, P. (PI);
Walbot, V. (PI);
Wang, Z. (PI);
Watanabe, J. (PI);
Watt, W. (PI);
Matus, O. (GP)
BIO 291:
Development and Teaching of Core Experimental Laboratories
Preparation for teaching the core experimental courses (44X and 44Y). Emphasis is on lab, speaking, and writing skills. Focus is on updating the lab to meet the changing technical needs of the students. Taken prior to teaching either of the above courses. May be repeated for credit. Prerequisite: selection by instructor.
Terms: Aut, Win
| Units: 1-2
| Repeatable
for credit
BIO 292:
Curricular Practical Training
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: Win, Spr, Sum
| Units: 1
| Repeatable
3 times
(up to 3 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.
Last offered: Spring 2018
| Units: 3
BIO 296:
TA Training in Biology
Workshop to provide teaching assistants in the Department of Biology with basic training, support, and professional development in their teaching roles. Should be taken concurrently with the first TA position.
Terms: Aut, Win, Spr
| Units: 1
BIO 299:
Biology PhD Lab Rotation
Limited to first year Biology PhD students. Lab rotations with Biosciences faculty.
Terms: Aut, Win, Spr, Sum
| Units: 1-10
| Repeatable
for credit
BIO 300:
Graduate Research
For graduate students only. Individual research by arrangement with in-department instructors.
Terms: Aut, Win, Spr, Sum
| Units: 1-10
| Repeatable
for credit
Instructors: ;
Barton, K. (PI);
Bergmann, D. (PI);
Berry, J. (PI);
Block, B. (PI);
Block, S. (PI);
Boggs, C. (PI);
Chen, X. (PI);
Crowder, L. (PI);
Cyert, M. (PI);
Daily, G. (PI);
De Leo, G. (PI);
Denny, M. (PI);
Dinneny, J. (PI);
Dirzo, R. (PI);
Dixon, S. (PI);
Ehrlich, P. (PI);
Feldman, J. (PI);
Feldman, M. (PI);
Fernald, R. (PI);
Field, C. (PI);
Fraser, H. (PI);
Frommer, W. (PI);
Frydman, J. (PI);
Fukami, T. (PI);
Gilly, W. (PI);
Goldbogen, J. (PI);
Gordon, D. (PI);
Gozani, O. (PI);
Grossman, A. (PI);
Hadly, E. (PI);
Hanawalt, P. (PI);
Heller, H. (PI);
Jones, P. (PI);
Jonikas, M. (PI);
Klein, R. (PI);
Kopito, R. (PI);
Long, S. (PI);
Lowe, C. (PI);
Luo, L. (PI);
McConnell, S. (PI);
Micheli, F. (PI);
Mooney, H. (PI);
Mordecai, E. (PI);
Morrison, A. (PI);
Mudgett, M. (PI);
Nelson, W. (PI);
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);
Roughgarden, J. (PI);
Sapolsky, R. (PI);
Schnitzer, M. (PI);
Shatz, C. (PI);
Shen, K. (PI);
Simon, M. (PI);
Simoni, R. (PI);
Skotheim, J. (PI);
Somero, G. (PI);
Stearns, T. (PI);
Tessier-Lavigne, M. (PI);
Thompson, S. (PI);
Ting, A. (PI);
Tsao, P. (PI);
Tuljapurkar, S. (PI);
Vitousek, P. (PI);
Walbot, V. (PI);
Wang, Z. (PI);
Watt, W. (PI)
BIO 300X:
Out-of-Department Graduate Research
Individual research by arrangement with out-of-department instructors. Master's students: credit for work arranged with out-of-department instructors is restricted to Biology students and requires approved department petition. See http://biohonors.stanford.edu for more information. May be repeated for credit.
Terms: Aut, Win, Spr, Sum
| Units: 1-10
| Repeatable
for credit
Instructors: ;
Axelrod, J. (PI);
Barna, M. (PI);
Bergmann, D. (PI);
Bertozzi, C. (PI);
Bhatt, A. (PI);
Bintu, L. (PI);
Block, B. (PI);
Block, S. (PI);
Brandman, O. (PI);
Brunet, A. (PI);
Bustamante, C. (PI);
Cegelski, L. (PI);
Cimprich, K. (PI);
Clandinin, T. (PI);
Contag, C. (PI);
Crowder, L. (PI);
Curtis, C. (PI);
Cyert, M. (PI);
Daily, G. (PI);
Davis, R. (PI);
Demirci, U. (PI);
Denny, M. (PI);
Ding, J. (PI);
Dirzo, R. (PI);
Ehrlich, P. (PI);
Feldman, M. (PI);
Fernald, R. (PI);
Field, C. (PI);
Fire, A. (PI);
Fraser, H. (PI);
Frommer, W. (PI);
Frydman, J. (PI);
Fukami, T. (PI);
Fuller, M. (PI);
Gilly, W. (PI);
Gitler, A. (PI);
Gordon, D. (PI);
Gozani, O. (PI);
Hadly, E. (PI);
Hanawalt, P. (PI);
Heller, H. (PI);
Huang, P. (PI);
Jackson, P. (PI);
Jarosz, D. (PI);
Jones, P. (PI);
Khavari, P. (PI);
Khosla, C. (PI);
Kopito, R. (PI);
Krasnow, M. (PI);
Kuo, C. (PI);
Lin, M. (PI);
Long, J. (PI);
Long, S. (PI);
Lowe, C. (PI);
Luo, L. (PI);
McConnell, S. (PI);
Micheli, F. (PI);
Montgomery, S. (PI);
Mordecai, E. (PI);
Morrison, A. (PI);
Mudgett, M. (PI);
Nelson, W. (PI);
O'Brien, L. (PI);
O'hara, R. (PI);
Palumbi, S. (PI);
Petrov, D. (PI);
Pringle, J. (PI);
Puglisi, J. (PI);
Rando, T. (PI);
Red-Horse, K. (PI);
Rosenberg, N. (PI);
Salzman, J. (PI);
Sapolsky, R. (PI);
Scherrer, G. (PI);
Schnitzer, M. (PI);
Sebastiano, V. (PI);
Shapiro, L. (PI);
Shatz, C. (PI);
Shen, K. (PI);
Shenoy, K. (PI);
Sherlock, G. (PI);
Simon, M. (PI);
Skotheim, J. (PI);
Stearns, T. (PI);
Steinman, L. (PI);
Straight, A. (PI);
Theriot, J. (PI);
Thompson, S. (PI);
Tuljapurkar, S. (PI);
Vitousek, P. (PI);
Walbot, V. (PI);
Wang, B. (PI);
Wernig, M. (PI);
Wu, J. (PI);
Wysocka, J. (PI);
Johnson, S. (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, Spr
| Units: 1-3
| Repeatable
for credit
BIO 302:
Current Topics and Concepts in Population Biology, Ecology, and Evolution
Required of first-year PhD students in population biology, and ecology and evolution. Major conceptual issues and developing topics. This course isnnopen only to Biology PhD students and is not open to auditors."
Terms: Aut
| Units: 1
BIO 303:
Current Topics and Concepts in Population Biology, Ecology, and Evolution
Required of first-year PhD students in population biology, and ecology and evolution. Major conceptual issues and developing topics. This course isnnopen only to Biology PhD students and is not open to auditors."
Terms: Win
| Units: 1
BIO 304:
Current Topics and Concepts in Population Biology, Ecology, and Evolution
Required of first-year PhD students in population biology, and ecology and evolution. Major conceptual issues and developing topics. This course isnnopen only to Biology PhD students and is not open to auditors.
Terms: Spr
| Units: 1
BIO 313:
Ethics in the Anthropocene
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.
Terms: Spr
| Units: 1
BIO 329:
Matrix Methods for Dynamic Models and Data Analysis
Types of matrices in dynamic & stochastic models, covariances, rectangular data, networks. Spectral theorem, asymptotics, stability theory, Nonnegative matrices, ergodicity, Markov chains. Hermitian, covariance, SVD. Perturbation theory. Random matrix products, Lyapunov exponents. Open to Ph.D. students in Biology. Prerequisites: Calculus (AP level) required. Some knowledge of linear algebra, R, preferred.
Last offered: Autumn 2016
| Units: 1
BIO 330:
Stochastic Methods for Simulation, Dynamics and Data Analysis
Markov chains: ergodicity, CLT, passage times, absorption. Simulation: random numbers, chains. Poisson processes: applications and simulation. Time series models. MCMC essentials. Open to Ph.D. students in Biology. Prerequisites: Calculus (AP level) and basic linear algebra required. Facility with linear algebra, R, preferred.
Last offered: Winter 2017
| Units: 1
BIO 332:
Evolutionary Genomics
We will read classic and modern papers relevant to evolutionary genomics, and discuss. We will cover a broad range of topics, methods, and species.
Terms: Win
| Units: 2
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.
Terms: Win, Spr
| Units: 1-3
| Repeatable
for credit
BIO 346:
Advanced Seminar on Prokaryotic 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.
Terms: Spr
| 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 consider how advances in genome technology have enabled new explorations in conservation and population biology. Papers to be read will include technical applications of new genome tools, the role of bioinformatics, and long-standing questions in conservation and population biology that might now be answered.
Terms: Aut, Spr
| Units: 1
BIO 459:
Frontiers in Interdisciplinary Biosciences (BIOC 459, BIOE 459, CHEM 459, CHEMENG 459, PSYCH 459)
Students register through their affiliated department; otherwise register for CHEMENG 459. For specialists and non-specialists. Sponsored by the Stanford BioX Program. Three seminars per quarter address scientific and technical themes related to interdisciplinary approaches in bioengineering, medicine, and the chemical, physical, and biological sciences. Leading investigators from Stanford and the world present breakthroughs and endeavors that cut across core disciplines. Pre-seminars introduce basic concepts and background for non-experts. Registered students attend all pre-seminars; others welcome. See http://biox.stanford.edu/courses/459.html. Recommended: basic mathematics, biology, chemistry, and physics.
Terms: Aut, Win, Spr
| Units: 1
| Repeatable
for credit
BIO 802:
TGR Dissertation
Terms: Aut, Win, Spr, Sum
| Units: 0
| Repeatable
for credit
Instructors: ;
Baker, B. (PI);
Barton, K. (PI);
Bergmann, D. (PI);
Berry, J. (PI);
Block, B. (PI);
Block, S. (PI);
Boggs, C. (PI);
Chen, X. (PI);
Crowder, L. (PI);
Cyert, M. (PI);
Daily, G. (PI);
De Leo, G. (PI);
Denny, M. (PI);
Dinneny, J. (PI);
Dirzo, R. (PI);
Dixon, S. (PI);
Ehrlich, P. (PI);
Epel, D. (PI);
Feldman, J. (PI);
Feldman, M. (PI);
Fernald, R. (PI);
Field, C. (PI);
Fraser, H. (PI);
Frommer, W. (PI);
Frydman, J. (PI);
Fukami, T. (PI);
Gilly, W. (PI);
Goldbogen, J. (PI);
Gordon, D. (PI);
Gozani, O. (PI);
Grossman, A. (PI);
Hadly, E. (PI);
Hanawalt, P. (PI);
Heller, H. (PI);
Jones, P. (PI);
Jonikas, M. (PI);
Klein, R. (PI);
Kopito, R. (PI);
Long, S. (PI);
Lowe, C. (PI);
Luo, L. (PI);
McConnell, S. (PI);
Micheli, F. (PI);
Mooney, H. (PI);
Mordecai, E. (PI);
Morrison, A. (PI);
Mudgett, M. (PI);
Nelson, W. (PI);
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);
Roughgarden, J. (PI);
Sapolsky, R. (PI);
Schnitzer, M. (PI);
Shatz, C. (PI);
Shen, K. (PI);
Simon, M. (PI);
Simoni, R. (PI);
Skotheim, J. (PI);
Somero, G. (PI);
Stearns, T. (PI);
Tessier-Lavigne, M. (PI);
Thompson, S. (PI);
Ting, A. (PI);
Tuljapurkar, S. (PI);
Vitousek, P. (PI);
Walbot, V. (PI);
Wang, Z. (PI);
Watt, W. (PI);
Wong, W. (PI)
