printer friendly pageBIO 268: Statistical and Machine Learning Methods for Genomics (BIOMEDIN 245, CS 373, STATS 345)
Introduction to statistical and computational methods for genomics. Sample topics include: expectation maximization, hidden Markov model, Markov chain Monte Carlo, ensemble learning, probabilistic graphical models, kernel methods and other modern machine learning paradigms. Rationales and techniques illustrated with existing implementations used in population genetics, disease association, and functional regulatory genomics studies. Instruction includes lectures and discussion of readings from primary literature. Homework and projects require implementing some of the algorithms and using existing toolkits for analysis of genomic datasets.
Last offered: Winter 2020
BIO 269: Comparative Single-cell Genomics in the Ocean (BIOE 269)
The goal of the course is to provide students with hands-on experience in applying single-cell sequencing technology to examine marine animals with cellular resolution, both at the bench and on computers. Throughout the course, students learn how to collect animals, dissect and dissociate tissues, generate single-cell sequencing libraries, process and analyze their own data, and compare cell types across animals using the computational pipelines. This pipeline is optimized to study organisms without extensive prior knowledge and provides students with a valuable set of tools for future work in this field. This course uses a diverse set of animals in order to study the conservation and divergence of cell types and their gene regulatory programs across the animal kingdom. The course includes lectures on Mondays, and web and dry lab components, which have flexible schedules. Pre-requite:
BioE219 (recommended for engineering students) or instructor consent.
Last offered: Summer 2023
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
Instructors:
Tuljapurkar, S. (PI)
BIO 273A: Environmental Microbiology I (CEE 274A, CHEMENG 174, CHEMENG 274)
Basics of microbiology and biochemistry. The biochemical and biophysical principles of biochemical reactions, energetics, and mechanisms of energy conservation. Diversity of microbial catabolism, flow of organic matter in nature: the carbon cycle, and biogeochemical cycles. Bacterial physiology, phylogeny, and the ecology of microbes in soil and marine sediments, bacterial adhesion, and biofilm formation. Microbes in the degradation of pollutants. Prerequisites:
CHEM 33,
CHEM 121 (formerly
CHEM 35), and BIOSCI 83,
CHEMENG 181, or equivalents.
Last offered: Autumn 2020
BIO 273B: Microbial Bioenergy Systems (CEE 274B, CHEMENG 456)
Introduction to microbial metabolic pathways and to the pathway logic with a special focus on microbial bioenergy systems. The first part of the course emphasizes the metabolic and biochemical principles of pathways, whereas the second part is more specifically directed toward using this knowledge to understand existing systems and to design innovative microbial bioenergy systems for biofuel, biorefinery, and environmental applications. There also is an emphasis on the implications of rerouting of energy and reducing equivalents for the fitness and ecology of the organism. Prerequisites:
CHEMENG 174 or 181 and organic chemistry, or equivalents.
Last offered: Winter 2020
BIO 273H: Marine Conservation Biology (BIO 173H, OCEANS 173, OCEANS 173H, OCEANS 273H)
Class can be taken in person or via Zoom. Introduction to the key concepts of ecology and policy relevant to marine conservation issues at the population to ecosystems level. Focus on the origin and maintenance of biodiversity and conservation applications from both the biology and policy perspectives (for example, endangered species, captive breeding, reserve design, habitat fragmentation, ecosystem restoration/rehabilitation). Also includes emerging approaches such as ecosystem-based management, ocean planning, and coupled social-ecological systems. The course will include lectures, readings and discussions of primary literature, and attendance at seminars with visiting scholars. Prerequisite: introductory biology; suggested: a policy and/or introductory ecology course. Students who want to enroll only in the seminar and discussion course (2 units) should register for OCEANS/BIO 173HA. (Graduate students register for BIO/
OCEANS 273H.) For information on how to spend spring quarter i
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Class can be taken in person or via Zoom. Introduction to the key concepts of ecology and policy relevant to marine conservation issues at the population to ecosystems level. Focus on the origin and maintenance of biodiversity and conservation applications from both the biology and policy perspectives (for example, endangered species, captive breeding, reserve design, habitat fragmentation, ecosystem restoration/rehabilitation). Also includes emerging approaches such as ecosystem-based management, ocean planning, and coupled social-ecological systems. The course will include lectures, readings and discussions of primary literature, and attendance at seminars with visiting scholars. Prerequisite: introductory biology; suggested: a policy and/or introductory ecology course. Students who want to enroll only in the seminar and discussion course (2 units) should register for OCEANS/BIO 173HA. (Graduate students register for BIO/
OCEANS 273H.) For information on how to spend spring quarter in residence:
https://hopkinsmarinestation.stanford.edu/undergraduate-studies/spring-courses-23-24 (Individual course registration also permitted.) Depending on enrollment numbers, a weekly shuttle to Hopkins or mileage reimbursements for qualifying carpools will be provided; terms and conditions apply.
Terms: Spr
| Units: 3
| Repeatable
for credit
(up to 99 units total)
Instructors:
Crowder, L. (PI)
;
Parker, Q. (TA)
BIO 274S: Hopkins Microbiology Course (CEE 274S, ESS 253S, OCEANS 274)
Four-week, intensive. The interplay between molecular, physiological, ecological, evolutionary, and geochemical processes that constitute, cause, and maintain microbial diversity. How to isolate key microorganisms driving marine biological and geochemical diversity, interpret culture-independent molecular characterization of microbial species, and predict causes and consequences. Laboratory component: what constitutes physiological and metabolic microbial diversity; how evolutionary and ecological processes diversify individual cells into physiologically heterogeneous populations; and the principles of interactions between individuals, their population, and other biological entities in a dynamically changing microbial ecosystem. Prerequisites:
CEE 274A and
CEE 274B, or equivalents. Formerly
BIOHOPK 274H.
Last offered: Summer 2021
| Repeatable
for credit
BIO 276: The Developmental Basis of Animal Body Plan Evolution (BIO 176)
Animals are grouped into phyla with defined organizational characteristics such as multicellularity, axis organization, and nervous system organization, as well as morphological novelties such as eyes, limbs and segments. This course explores the developmental and molecular origins of there animal innovations. Offered alternate years. Prerequisites: None.
Last offered: Winter 2022
BIO 278: Microbiology Literature (BIO 178)
For advanced undergraduates and first-year graduate students. Critical reading of research literature in prokaryotic genetics and molecular biology. Classic and foundational papers in pathogenesis, bacterial and phage genetics, and molecular biology; recent literature on gene regulation. Diverse experimental approaches: biochemistry, genomics, pathogenesis, and cell biology. Prerequisites: undergraduates must have taken
BIO 82 (Genetics) and
BIO 83 (Biochemistry). Also recommended:
BIO 111,
BIO 120,
CEE 274. Undergraduate enrollment is limited to Biology or Bioengineering majors in junior or senior year. Co-term or Ph.D. students in basic life sciences departments such as Biology, Bioengineering, and Genetics may enroll in
BIO 278 for graduate credit. Enrollment by permission of professor, apply at
https://forms.gle/fnBTL58QE8H5H22X8.
Terms: Aut
| Units: 3
Instructors:
Long, S. (PI)
BIO 279: The Science & Practice of Valuing Nature for a Better World (BIO 179, EARTHSYS 179, EARTHSYS 279)
This course explores the science of valuing nature, through two interwoven pathways. One is biophysical, focused on human dependence and impacts on Earth's life-support systems. If well managed, lands, waters, and biodiversity yield a flow of vital benefits that sustain and fulfill human life. We will develop a framework and practical tools for quantifying this stream of benefits from nature to people. The second pathway is social, economic, and philosophical, weaving through concepts of well-being, human development, and conservation and the ethics and effects of their pursuit. We will look back, ahead into the future, and inward, taking a global view and considering diverse cultural perspectives. Our discussions will be situated in the context of the COVID-19 pandemic, movements for racial justice and socioeconomic equity, and efforts to enable people and nature to thrive in cities and countries worldwide. The course is intended for diverse, advanced students, with interests in resea
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This course explores the science of valuing nature, through two interwoven pathways. One is biophysical, focused on human dependence and impacts on Earth's life-support systems. If well managed, lands, waters, and biodiversity yield a flow of vital benefits that sustain and fulfill human life. We will develop a framework and practical tools for quantifying this stream of benefits from nature to people. The second pathway is social, economic, and philosophical, weaving through concepts of well-being, human development, and conservation and the ethics and effects of their pursuit. We will look back, ahead into the future, and inward, taking a global view and considering diverse cultural perspectives. Our discussions will be situated in the context of the COVID-19 pandemic, movements for racial justice and socioeconomic equity, and efforts to enable people and nature to thrive in cities and countries worldwide. The course is intended for diverse, advanced students, with interests in research and in moving from science to action for a more just and sustainable world. Prerequisite: Basic to intermediate GIS (Geographic Information Systems) skills are necessary. We will help with these, but not teach GIS specifically in class. Basic skills include, for example: working with raster, vector and tabular data; loading rasters, shapefiles, and tables into a GIS; changing the symbology of rasters and shapefiles in your chosen GIS; editing raster and shapefile attribute tables; understanding coordinate systems and how to re-project layers; looking at individual raster cell values; and performing basic raster math.
Terms: Aut
| Units: 1-3
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