Biology
Contact Information
Faculty and their Research Interests
Modern biological research demands an interdisciplinary approach to address the most important problems. The Department of Biology is dedicated to the study ofbiological questions at all levels. Current research in the department spans a broad spectrum and includes:
• Cell, Molecular, Developmental and Plant Biology: protein folding, single molecule biophysics, regulation of gene expression, cell migration, signaling, intracellular protein trafficking, cytoskeleton, cell cycle
• Integrative, Organismal and Marine Biology: thermoregulation, sensory transduction, development, behavior
• Ecology, Evolution and Population Biology: ecology biodiversity, adaptation, evolution, conservation biology
The diverse range of interests and expertise in the department creates a challenging intellectual environment that encourages students to take innovative approaches to the study of fundamental questions in biology. The department trains its Ph.D. candidates for careers in basic research, offering intensive instruction in laboratories, seminars, and teaching.
The Department of Biology is located geographically in the heart of the Stanford campus in close proximity to the departments of chemistry, physics, the School of Engineering, the School of Medicine, and the School of Earth Sciences. The department includes Hopkins Marine Station, located on the Monterey peninsula, which is dedicated to the study of marine organisms, and the Jasper Ridge Biological Preserve, a natural preserve close to the Stanford campus. The department also has close ties with the Carnegie Institution of Washington’s Departments of Plant Biology and Global Ecology, a private research institution located on the Stanford campus.
The mission of the Department of Biology is to mentor and educate biology students at the graduate, undergraduate, and post-doctoral level. Scientific interactions between research groups are fostered through an annual retreat, a weekly seminar series, and weekly research presentations by graduate students and post-doctoral fellows in the department. To accommodate the broad range of interests, three distinct academic tracks are offered for graduate study:
I. CELL, MOLECULAR,
DEVELOPMENTAL,
AND PLANT BIOLOGY
Students in this area apply cutting-edge techniques in genetics, cell biology, biochemistry, biophysics, plant biology and neurobiology to the study of basic biological phenomena. Faculty research in this segment of the department covers a wide range of topics including: protein folding and turnover, nuclear transport, regulation of the cell cycle and cytoskeleton, intracellular signaling, development and function of the nervous system, plant-microbe interactions, and plant development.
Graduate students spend their first year taking classes and carrying out research rotations in three different laboratories of their choosing. At the end of the first year, students choose a lab in which to carry out their doctoral research, and the rest of their time in the department is devoted primarily to designing and executing original research under the mentorship of their doctoral advisor and a thesis committee.
II. INTEGRATIVE, ORGANISMAL AND MARINE BIOLOGY
Graduate students in this area have the opportunity to study a range of topics in physiology, neurophysiology and marine biology. In their first year, students take classes and have the option to carry out research rotations before choosing a lab in which to carry out their thesis research. Students gain experience in undergraduate teaching, and focus intensively on original research conducted under the mentorship of their doctoral advisor and a thesis committee.
Many of the faculties in this track are at Hopkins Marine Station, a research facility located in Pacific Grove, about 90 miles south of the Stanford campus. Graduate students interested in working with a faculty member at the Marine Station spend part of their first year taking courses on the main Stanford campus. The Marine Station is an independent campus with fully equipped modern laboratories and an excellent library. Both field and laboratory studies at Hopkins emphasize the unique adaptations of marine animals and plants to the intertidal, subtidal, deep-sea and coastal environments. Other research efforts use marine organisms in basic molecular, cellular and physiological studies.
III. ECOLOGY, EVOLUTION,
AND POPULATION BIOLOGY
Students in this area study a broad range of conceptual and empirical questions from ecology, evolutionary biology and evolutionary genetics. Research groups work with a diversity of organisms, including bacteria, plants, birds, insects, reptiles, and marine invertebrates. Approaches are varied, and include field studies, laboratory investigations, computer modeling and mathematical analyses. Research groups in this segment of the department benefit from access to the nearby Jasper Ridge Biological Preserve. Jasper Ridge is a remarkable 1,189 acre preserve of plants and animals native to California, and has been used for research for over a century. The graduate student training program is tailored individually to each student, and emphasizes the development of research, communication, and teaching skills.
For more information contact:
Student Services
Department of
Biology
Gilbert Building, Room 108
371 Serra Mall
Stanford, CA 94305-5020
(650) 723-1826
(650) 723-6132 (fax)
biologyadmissions@stanford.edu
http://biology.stanford.edu/
Faculty and their Research Interests
Cell, Molecular, Developmental and Plant Biology
Kathryn Barton, by courtesy 1. Stem cells in plants, formation of leaves and their development into flattened, polarly differentiated organs, role of small RNAs in leaf and stem cell development, embryogenesis in plants.
http://www-ciwdpb.stanford.edu/research/research_barton.php
Dominique Bergmann. We use genetic, genomic and cell biological approaches to study how cells acquire specific fates and how those cells are patterned in a complex tissue. Our current work is focused on stomatal development as a paradigm for understanding how multiple sources of information—from cell lineage, cell-cell communication and from the environment—are integrated into the appropriate cell fate and cell proliferation responses.
Steven M. Block3. Properties of proteins or nucleic acids at the level of single macromolecules and molecular complexes. Experimental tools include laser-based optical traps (“optical tweezers”) and a variety of state-of-the-art fluorescence techniques, in conjunction with custom-built instrumentation for the nanometer-level detection of displacements and piconewton-level detection of forces.
http://www.stanford.edu/group/blocklab/
William F. Burkholder. Our lab is interested in how bacteria monitor and coordinate cell cycle events. We are focused on identifying and characterizing signal transduction pathways used by the bacterium Bacillus subtilis to regulate cell cycle progression and development in response to chromosome status. Our goal is to understand how these pathways work mechanistically and how they contribute to normal growth, development, and genome stability.
http://burkholder.stanford.edu/
Allan M. Campbell. Comparative molecular biology of DNA insertion by bacteriophage lambda and its relatives, analyzing the organization of the biotin operon in Escherichia coli, and the genetic control of related pathways. Phage integration is a model system for the catalysis and regulation of specific DNA rearrangements.
Martha Cyert. We study Ca2+ regulated signal transduction mediated by the highly conserved, Ca2+/calmodulin-regulated phosphatase, calcineurin.. Genetic, biochemical, genomic, and proteomic approaches are employed to identify calcineurin substrates and regulators comprehensively in Saccharomyces cerevisiae, to study substrate recognition by calcineurin, and to examine physiological processes that are regulated by calcineurin in vivo.
http://www.stanford.edu/group/cyert/
Wolf Frommer, by courtesy1. Focus: Signaling networks for controlling and integrating metabolite transport and metabolism. Tools: FRET-based nanosensors for imaging metabolites in living organisms using confocal fluorescence microscopy; phosphoproteomics; membrane protein interactome, siRNA. Goals: Identify regulatory and model networks. Model systems: yeast, mammalian cell cultures and Arabidopsis.
Judith Frydman. We use a highly interdisciplinary approach to understand how molecular chaperones facilitate correct protein folding and prevent protein misfolding and aggregation in eukaryotic cells. Understanding how chaperones maintain normal protein homeostasis and facilitate degradation of misfolded proteins will have important implications for understanding of a growing list of protein folding diseases.
http://www.stanford.edu/group/frydman/ or http: //proteinfoldingcenter.org/
Or Gozani. Research in the Gozani lab aims to understand how alterations in chromatin structure are sensed and transduced to effect diverse biological outcomes, and how disruption in these mechanisms can lead to pathologic states. Questions are addressed utilizing a combination of biochemical, molecular and cell biological approaches.
Arthur R. Grossman, by courtesy1. How photosynthetic organisms acclimate to their environment and adjust the physiology of the cell. Effects of light are studied in cyanobacteria. Effects of changes in nutrients such as sulphur and phosphorus are studied in mutant green algae and cyanobacteria which are unable to acclimate to nutrient limitation.
http://carnegiedpb.stanford.edu/research/grossman2003_rev1/index.html
Philip C. Hanawalt. Cellular processing of damaged DNA and non-canonical DNA structures during transcription and replication. Mechanism and consequences of transcription-coupled DNA repair. Genetic control of DNA repair . Relationships of DNA repair deficiencies to cancer, aging and human genetic disease.
http://www.stanford.edu/~hanawalt/
Patricia P. Jones. Genetic, cellular, and molecular mechanisms that regulate adaptive immune responses (the antigen-specific responses carried out by B and T lymphocytes, unique to vertebrates), and innate immune responses (responses present triggered by microbial components in both invertebrates and vertebrates.)
Ron R. Kopito. Cellular mechanisms which monitor protein biogenesis and ensure that only properly folded and assembled proteins are deployed within the cell. Genetic biochemical and cell biological approaches are used to identify the machinery involved in recognizing and destroying misfolded proteins.
http://www.stanford.edu/group/kopito
Sharon R. Long. Molecular, genetic, and biochemical techniques are used to study how Rhizobium cells recognize and form nodules on their plant hosts. The association is highly specific and involves complex transcriptional and cellular responses by both the bacterium and eukaryotic host.
http://cmgm.stanford.edu/biology/long/
Liqun Luo. We use molecular genetics to understand the logic of neural circuit organization and assembly in fruit flies and mice. For additional information, see:
http://www.stanford.edu/group/luolab.
Susan K. McConnell. We are interested in how individual neurons know where they should sit in the mammalian brain and with which neurons they should form specific axonal connections. We are characterizing the progenitor cells that give rise to neurons and the processes by which young neurons locate their correct targets among hundreds of thousands of other neurons in the brain.
http://www.stanford.edu/group/skmlab/
Ashby Morrison. Our research interests are to elucidate the contribution of chromatin to mechanisms that promote genomic integrity. The regulation of chromatin is a crucial component of DNA metabolism and processing in eukaryotic organisms. We utilize an integrated approach of genetic, biochemical, and molecular techniques, in both yeast and mammalian systems, to examine the involvement of chromatin in processes that prevent genome instability and the pathogenesis of disease.
http://www.stanford.edu/group/morrison
Mary Beth Mudgett. Biochemical and genetic basis of microbial pathogenesis and disease resistance in plants. Research program aimed to elucidate of the function of Xanthomonas type III virulence factors in susceptible tomato hosts.
http://www.stanford.edu/~mudgett/
W. James Nelson10. Our research objectives are to understand cellular mechanisms involved in development and maintenance of cell polarity. Recent studies indicate that development of epithelial cell polarity is a multistage process requiring instructive extracellular cues (eg. cell-cell and cell-substratum contact) and reorganization of proteins in the cytoplasm and on the plasma membrane. Once established, polarity is maintained by targeting and retention of proteins to functionally distinct apical and basal-lateral plasma membrane domains.
Carla J. Shatz11. The major goal of research in the Shatz Laboratory is to discover cellular and molecular mechanisms that transform early fetal and neonatal brain circuits into mature connections, and in particular to determine the extent to which neural function during critical periods of development is needed for these circuits to tune up into adult patterns of connectivity.
http://www.stanford.edu/group/shatzlab
Kang Shen. We are interested in understanding how synapses are formed, the final step in wiring a nervous system. In particular, the molecular mechanisms underlying synaptic specify: how neurons recognize each other and how they make decisions about forming synapses between contacting neurites during development. We use molecular, genetic and cell biological tools to study this question in the nematode, C. elegans, which has a very simple nervous system containing only 302 neurons and approximately 6000 synapses.
Michael A. Simon. We use genetic and biochemical approaches to study three areas of developmental biology; planar cell polarity (PCP) in epithelial cells, control of cell shape, motility and the actin cytoskeleton by Src family protein tyrosine kinases, and control of cell fate specification by receptor tyrosine kinases.
http://www.stanford.edu/group/simonlab/
Robert D. Simoni. The nature of cellular membranes using a broad range of techniques, from molecular biology and biochemistry to cell biology. We continue to analyze the role of cholesterol in biological membranes, as well as the genetic mechanisms by which cholesterol production is regulated. This study has direct clinical relevance to the problems of atherosclerosis and heart disease.
Jan M. Skotheim. In vivo fluorescence optical imaging, genetic and computational analysis of cell cycle control in yeast and mammalian systems. The laboratory aims to understand the principles underlying natural genetic control networks, which will aid design of synthetic systems.
Alfred M. Spormann, by courtesy7. Molecular mechanisms of microbial degradation of unusual organic compounds, for example organic pollutants. Also the molecular mechanism of gliding motility in bacteria.
http://www.stanford.edu/group/spormannlab
Tim P. Stearns. The central question in our work is how cells accurately segregate their genome at each cell division. The work is focused on the centrosome, a unique organelle at the center of the cell that organizes the cytoskeleton and serves as a site for integration of cellular signals. We use the tools of cell biology, genetics, and biochemistry in systems ranging from yeast to human cells to understand how the centrosome duplicates once per cell cycle, and how centrosome defects are involved in the genome instability that is observed in many types of cancer.
http://www.stanford.edu/~stearns/
Virginia Walbot. Our laboratory studies the behavior of MuDR/Mu transposons of maize to answer fundamental questions about transposon regulation and plant development. Without a fixed body size, how do plant cells cease division and how are Mu element excisions restricted to the final cell divisions? Plants lack a germ line, but a few floral cells differentiate to undergo meiosis - why does Mu transposition outcome change in pre-meiotic cells?
http://www.stanford.edu/~walbot/
Zhiyong Wang, by courtesy1. Molecular genetics and proteomics of signal transduction in plants.
http://carnegiedpb.stanford.edu/research/research_wang.php
Irving L. Weissman, by courtesy6. Developmental biology, self-renewal, homing and functions of the cells that make up blood-forming and immune systems.
Charles Yanofsky8. Studies are focused on two major problems: 1) Determining the features of the attenuation regulatory mechanism used by E. coli to control transcription of the degradative tryptophanase operon; 2) Determining the features of the transcriptional and translational regulatory mechanisms controlling expression of operons concerned with tryptophan biosynthesis in B. subtilis. Both studies are revealing novel features of gene regulation.
Integrative, Organismal and Marine Biology
Barbara A. Block2. The Block lab investigates endothermy in fish including cellular, ecological and evolutionary physiology. Cellular basis for endothermic metabolism. Research at sea is focused on understanding the movements and physiological ecology of tunas and billfishes to gain insight into the selective advantage of endothermy in fish and habitat utilization.
http://hms.stanford.edu/block.htm
Mark W. Denny2. Mechanical design of intertidal organisms. This subject is studied at many different levels of organization, from the molecular, through the material, structural, and organismal, to the ecological.
http://www.stanford.edu/group/denny/
David Epel2, 8. How development takes place in the marine environment, especially how embryos resist the effects of such environmental stresses as ultraviolet radiation, pathogens and natural and man-made toxins. How can the oocyte or the few-celled embryo protect itself from pathogens such as bacteria, ultraviolet radiation, or the effects of toxins, both natural and manmade?
http://www.stanford.edu/~depel/
Russell D. Fernald. In the course of evolution, two of the strongest selective forces in nature, light and sex, have left their mark on living organisms. I am interested in how the evolution and function of the nervous system reflects these events. In the visual system, we are studying how eyes evolved. In the reproductive system, we have identified a collection of cells in the brain containing gonodotropin releasing hormone (GnRH) that respond to changes in the social conditions by changing size.
William F. Gilly2. Neural control of behavioral and physiological mechanisms of hypoxia-tolerance in squid; biology of cone snails, structure and function of natural toxins that target voltage-gated ion channels.
http://gilly.stanford.edu/home.html
H. Craig Heller. Neurobiology of sleep, circadian rhythms, and learning; regulation of body temperature, mammalian hibernation, and human exercise physiology. Dr. Heller's laboratory is interested in questions about the function of sleep and circadian rhythms, and that has led to investigations of the role of sleep and rhythms on learning. His laboratory collaborates with that of Dr. Craig Garner in the Dept. of Psychiatry and Behavioral Science on the mechanisms of learning disabilities especially in Down Syndrome and Alzheimer's Disease. Research on human exercise physiology focuses on the effects of body temperature on physical conditioning and performance. His laboratory has developed technologies for manipulating body temperature for medical, protective, and performance applications.
Chris Lowe2. My research interests are in the field of evolution and development, and more specifically the evolution of the deuterostomes. My lab is currently investigating three major areas: The origin and evolution of the vertebrate brain and head. The early evolution of the deuterostome endoderm and mesoderm. The evolution of posterior growth in bilaterians.
http://www.lowelab.org/Lowe_Lab/Home.html
Fiorenza Micheli2. We study the processes and interactions shaping coastal marine communities and how to incorporate this understanding in the management and conservation of marine ecosystems. We are most interested in how disturbance and interactions between species underlie the organization, spatial variation, and temporal change in marine communities. Our research also seeks to apply community ecology to increase our understanding of human impacts on the marine environment and to design conservation and restoration strategies.
http://www.stanford.edu/group/MicheliLab/
Stephen R. Palumbi2. We study genetics, evolution, conservation, population biology and systematics in a wide variety of marine organisms. Primary focus is the use of molecular genetic techniques in conservation, including identification of dolphin and whale products in commercial markets. Also, molecular evolution of reproductive isolation and its influence on speciation.
http://www.stanford.edu/group/Palumbi/
Robert M. Sapolsky. How a neuron dies during aging or following various neurological insults; how such neuron death can be accelerated by stress; the design of gene therapy strategies to protect endangered neurons from neurological disease; the ability of parasites to alter brain function and thus manipulate host behavior.
Mark J. Schnitzer. In vivo fluorescence optical imaging and electrophysiological studies of the fly and mammalian brains towards understanding biophysical aspects of learning and memory. We are developing and applying novel imaging approaches such as multiphoton fluorescence endoscopy for examining individual neurons and dendrites, with emphasis on experiments in awake behaving animals.
George N. Somero2. We study how changes in protein sequence and gene expression enable organisms to succeed in diverse marine environments, including the Antarctic ocean and rocky intertidal habitats. By comparing homologous proteins from animals adapted to different temperatures, we have shown that only minor differences in habitat temperature are sufficient to favor evolutionary changes. Abilities to shift gene expression adaptively in response to environmental change vary among species and may be critical in setting tolerance limits.
http://hms.stanford.edu/somero.htm
Stuart H. Thompson2. Signal transduction mechanisms in neurons with the goal of better understanding how neurons process information. Signal cascades initiated by G-protein coupled receptors and regional specialization of function in neurons and the role that localized clusters of ion channels play in the processing of information by the cell.
http://hms.stanford.edu/thompson.htm
Ecology and Evolutionary Biology
Joseph A. Berry, by courtesy1. Physiological means by which plants adapt to environmental stress and climactic change, and photosynthetic mechanisms used by higher plants and algaes to fix carbon dioxide.
http://carnegiedpb.stanford.edu/research/research_berry.php
Carol L. Boggs. We are exploring how environmental variation affects life-history traits, population structure and dynamics, and species interactions in ecological and evolutionary time, using Lepidoptera. Current interests include (1) how resource allocation strategies interact with foraging and life history in variable environments to affect fitness and population dynamics; (2) the ecological and evolutionary dynamics of small populations, including population re-introductions; and (3) invasion biology, particularly the evolutionary and ecological effects of non-native species’ invasion into co-evolved systems.
Gretchen C. Daily4, 12. Forecasting biodiversity change in agricultural landscapes. Quantifying the production and value of ecosystem services, and the societal return on conservation investments. Characterizing cultural dimensions of value associated with Nature. Field research mostly in Hawai’i and Latin America.
http://www.stanford.edu/group/CCB/Staff/gretchen.htm
Rodolfo Dirzo. My current work on conservation biology emphasizes the need of complementing the traditional interests of the conservation of taxa with the increasingly needed conservation of ecological processes. Most of my tropical work is carried out in Mexico and Central Amazonia.
Paul R. Ehrlich. Conservation biology; ecology, evolution, and behavior of natural populations (especially of butterflies); human ecology and evolution.
http://www.stanford.edu/group/CCB/Staff/Ehrlich.html
Marcus W. Feldman. Evolution of complex genetic systems that can undergo both natural selection and recombination. Human demographic studies, particularly of the sex ratio. Human molecular evolution. The evolution of learning as one interface between modern methods in artificial intelligence and models of biological processes, including communication. The interaction of biological and cultural evolution, for example in the spread of food plant domestication across Europe, and the transmission of learned behaviors in contemporary groups.
http://www-evo.stanford.edu/
Christopher B. Field. Ecosystem responses to interacting global changes, controls on the carbon and energy balance of natural ecosystems, and ecology and biogeochemistry at the global scale.
http://dge.stanford.edu/DGE/CIWDGE/labs/fieldlab/
Daniel Fisher, by courtesy3. Theoretical research in cell biology, particularly dynamical phenomena, and quantitative aspects of evolutionary dynamics focusing on microbes.
Hunter Fraser. We study the regulation and evolution of gene expression using a combination of experimental and computational approaches. Our work brings together quantitative genetics, genomics, epigenetics, and evolutionary biology to achieve a deeper understanding of how genetic variation within and between species affects genome-wide gene expression and ultimately shapes the phenotypic diversity of life.
http://www.stanford.edu/~hbfraser/
Tadashi Fukami. Ecological and evolutionary community assembly, with emphasis on historical contingency in community structure, ecosystem functioning, biological invasion and ecological restoration, using experimental, theoretical and comparative methods involving bacteria, protists, fungi, plants and animals.
http://www.stanford.edu/~fukamit/
Deborah M. Gordon. We study how ant colonies are organized, how colonies interact with their neighbors, and use of genetic markers to measure reproductive success and gene flow in harvester ants.
http://www.stanford.edu/~dmgordon
Elizabeth A. Hadly. Evolution and ecology of animal populations over the last two million years, especially focusing on the last 10,000 years. We sequence DNA collected from subfossils from locations in North and South America.
http://www.stanford.edu/group/hadlylab/
Richard G. Klein9. Researches the archeological and fossil evidence for the evolution of human behavior. He has done fieldwork in Spain and especially in South Africa, where has excavated ancient sites and analyzed the excavated materials since 1969. He has focused on the behavioral changes that allowed anatomically modern Africans to spread to Eurasia about 50,000 years ago, where they swamped or replaced the Neanderthals and other non-modern Eurasians.
Harold A. Mooney. Ecosystem ecology, invasion biology, biodiversity science, impacts of global changes on biotic systems. Research in his laboratory is currently centered on the study of the impact of enhanced CO2 on ecosystem structure and function.
Dmitri A. Petrov. The Petrov laboratory uses a variety of experimental and theoretical approaches to study the evolution of genes and genomes. The main area of interest is the molecular population genetics of adaptation and genome evolution.
http://petrov.stanford.edu/
Terry L. Root, by courtesy12. Research interests include: synergistic effects of rapid climate disruption with other stressors on the viability of species over the next several centuries; examining rarity and extinction in plants and animals; determining possible actions needed, including triage, to minimize the number of species included in the incipient climate-disruption mass extinction; enhancing communications between scientists, policy makers and the general public.
Joan Roughgarden5. My laboratory studies the evolution of social behavior using a combination of theoretical and field studies. We use the mathematics of cooperative game theory and we study Anolis lizards in the Caribbean.
http://www.stanford.edu/group/roughlab/
Stephen H. Schneider. Climate change science (modeling past, current and future climates), integrated assessment of ecological and economic impacts of human-induced climate change, identifying viable climate mitigation and adaptation strategies, food/climate and other environmental/science public policy issues, and public understanding of science.
Shripad Tuljapurkar. Dynamics and evolution of populations, phenotypic traits, and genetic variation in animal and human populations; the nature, causes and maintenance of phenotypic variation. Human mortality and fertility change, demographic transitions, and human health and development.
Peter M. Vitousek. Nutrient cycling in tropical and temperate forests. Regulation of cycling of nitrogen, phosphorus, and several other nutrients by using chemical analysis of soil, water, and gas samples from field sites. The biogeochemistry of indigenous agriculture, biological invasion by exotic species, and sources of elements during long-term soil and ecosystem development in the Hawaiian Islands.
http://www.stanford.edu/group/Vitousek/
Ward B. Watt. Developing evolutionary theory from mechanistic viewpoints. Using techniques ranging from biochemistry, DNA sequencing, and wind-tunnel flight biophysics to field ecology and mathematical population genetics, we study biochemical and physiological mechanisms of genetic variation, ecological niche structure as the source of natural-selective pressures, and the resulting patterns of evolution of metabolic organization.
1. Carnegie Institution of Washington
2. Hopkins Marine Station
3. Joint appointment with Applied Physics
4. Joint appointment with Institute for International Studies
5. Joint appointment with Geophysics
6. Joint appointment with Developmental Biology
7. Department of Civil Engineering
8. Active Emeriti
9. Joint appointment with Anthropology
10. Joint appointment with Molecular and Cellular Physiology
11. Joint appointment with Neurobiology
12. Joint appointment with Woods Institute for the Environment