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One of the major goals of the department is to create a principal center of research and teaching in developmental biology. The establishment of the Department of Developmental Biology has provided a means for assembling a critical mass of scientists who are leading the thrust in developmental biology and who can train new leaders in the attack on fundamental problems of development.
The specific areas of study represented by the fifteen faculty members in the department include vertebrate embryology, developmental genetics with particular emphasis on microbial systems, Dictyostelium, Drosophila, the nematode and vertebrate systems. Research is aimed at a basic understanding of the molecular mechanisms underlying developmental decisions and the resulting morphogenetic processes. The discipline of developmental biology draws on molecular genetics, cell biology and biochemistry.
On October 4, 1985, the Board of Trustees approved the establishment of the Department of Developmental Biology in the Stanford University School of Medicine. The department received authorization to offer degree programs on November 9, 1989. The Arnold and Mabel Beckman Center for Molecular and Genetic Medicine opened in 1989. Housed in the Center are the Department of Developmental Biology and three interrelated academic groups: the Howard Hughes Medical Institute Unit in Molecular and Genetic Medicine, the Department of Molecular and Cellular Physiology and the Department of Biochemistry. The Beckman Center is adjacent to the Medical Center. Housing over 50 faculty members and their research teams, the Beckman Center is an exciting component of the Stanford research community.
The department has 15 faculty members that attack the questions of developmental biology through many exciting research studies:
Ben Barres
Neuron-Glial Interactions in the Developing CNS
Gerald Crabtree
Intracellular signaling during vertebrate development. Signaling
through Ca2+, Calineurin and NFAT in axonal guidance and the
development of the nervous and immune systems. Mechanisms of
specificity in intracellular signaling.
Margaret T. Fuller
Mechanism and control of cellular morphogenesis during
differentiation and development; assembly and function of the
cytoskeleton
David Hogness (Emeritus)
A. Dale Kaiser
Cell-cell interactions in development and morphogenesis
Seung K. Kim
Genetics of organ formation; pancreas developmental biology; mouse
models of diabetes and pancreatic cancer
Stuart K. Kim
Epithelial cell polarity, whole genome profiling of gene expression
patterns using DNA microarrays, and genetic control of cell fate in
C. elegans
David M. Kingsley
Genetic control of skeletal development; bone and joint patterning;
mouse and human arthritis; molecular analysis of vertebrate evolution
in threespine sticklebacks
Harley McAdams
Design and function of genetic regulatory networks from a total system perspective.
Roeland Nusse
Cell interactions during embryogenesis of Drosophila; genetic and invitro studies
of the Wnt signaling pathway
Matthew P. Scott
Molecular genetics of pattern formation and gene regulation in
Drosophila and mammalian development. Mechanisms of cerebellar
development and tumorigenesis
Lucy Shapiro
Control of timing and spatial organization during cell
differentiation
James A. Spudich
Biochemical, molecular genetic and structural studies of actin,
myosin and associated regulator proteins from eukaryotic cells
Anne Villeneuve
Genetic control of chromosome behavior during C. elegans development;
meiotic recombination
William Talbot
Genetic basis of axis formation and gastrulation in the zebrafish
embryo. Functional genomics in zebrafish.
Irving L. Weissman
Stem and progenitor cells in normal and leukemic development of the
blood and immune systems;and the role of CNS stem cells and
progenitor cells in the generation and regeneration of the brain
Ellen Porzig
Stanford University has a student enrollment of aproximately 14,000, of whom nearly half are graduate students. The Department of Developmental Biology has a current enrollment of 33 students. Our students are:
Erika Bustamante (Rotating)
Charles Chan (Weissman)
Frank Chan (Rotating)
Wendy Ching (Nusse)
Erin Davies (Fuller)
Madolyn Rogers (Barres)
Richard Daneman (Barres)
Kari Dickinson (Seung Kim)
Greg Chin (Villeneuve)
Pamela Colosimo(Kingsley)
Michael Gordon (Nusse)
Kyle Gurley (Kingsley)
Kim Harnish (Nusse)
Kim Hosemann (Kingsley)
Jeremy Heit (Seung Kim)
Karen Ho (Scott)
Dennis Ko (Scott)
Charlene Kon (Nusse)
Susan Wright Marino (Nusse)
Eric Nudleman (Kaiser)
Brian Null (Scott)
Luiz Pantalena-Filho (Kingsley)
Michael Povelones (Nusse)
Kirthi Reddy (Villeneuve)
Ronald Siu (Nusse)
Nitzan Sternheim (Talbot)
Heather Stickney (Talbot)
Brian Summers (Kingsley)
Stream Wang (Scott)
Ravit Weissman (Rotating)
Alissa Winzeler (Rotating)
Ian Woods (Talbot)
Other Graduate Students doing full-time research in the
department include:
Ryan Corcoran (Scott)
Ellen Judd (Shapiro)
Sherry Wang (Shapiro)
Chi-hwa Wu (Nusse)
The department welcomes scholars who have recently completed their Ph.D. or M.D. and wish to continue their training and broaden their professional experience. For the scholar, postdoctoral training provides an opportunity both to further professional preparation and research skills and to be exposed to new ideas in a stimulating academic environment. The faculty sponsor works with the postdoctoral fellow to devise a plan of research and to establish goals for the period of training, and provides ongoing consultation.
The postdoctoral fellows in the department provide a reservoir of knowledge and technical expertise. They participate in the many journal clubs and research discussions and are a valuable resource for the graduate student community. Our current postdoctoral fellows are:
Monica Colaiacovo (Villeneuve)
Esther Danenberg (Nusse)
Andreas Eizinger (Stuart Kim)
Zemer Gitai (Shapiro)
Kenneth Hillers (Villeneuve)
Yuichi Hori (Seung Kim)
Jimmy Jakobsen (Kaiser)
Leanne Jones (Fuller)
Andrew Ko (Seung Kim)
Hans Martin Pogoda (Talbot)
Catriona Logan (Nusse)
James Lund (Kim)
Douglas Mortlock (Kingsley)
Katie Peichel (Kingsley)
Carmen Robinett (Fuller)
Eric Rulifson (Nusse)
Kathleen Ryan (Shapiro)
Gillian Stanfield (Villeneuve)
Martin Thanbichler (Shapiro)
Patrick Viollier (Shapiro)
Roy Welch (Kaiser)
Gregor Zimmerman (Scott)
Alan Zhu (Scott)
Many high school and undergraduate students gain their first research experience working with graduate students and postdoctoral fellows in the laboratories in the department. The department welcomes these students and utilizes their help through work-study, the Undergraduate Research Opportunities (URO) program, the Youth Opportunities Program and independent study.
Lab and Research Assistants and Technicians
Christie Barnes
Media Production
Yvonne Cheng (Kaiser)
Research Assistant
Felicia Chu (Talbot)
Research Assistant
Manny Dela Cruz
Lab Assistant
Matthew Fish (Nusse & Scott)
Research Technician
Kate Guenther (Kingsley)
Research Specialist
Jeffrey Harris (Shapiro)
Research Technician
Janine Hartford (Scott)
Research Specialist
Barbara Hill (Scott)
Lab Assistant
Min Jiang ( Stuart Kim)
Research Assistant
Janet Jin (Scott)
Research Assistant
Michelle Johnson (Kingsley)
Animal Care Assistant
Lauren Jow (Talbot)
Research Assistant
Austin Jou (Nusse)
Research Associate
Peter Kelly (Talbot)
Research Assistant
Monika Kiraly (Stuart Kim)
Scientific Programmer
Paul Kunst
Media & Glassware Supervisor
Dominic Lee
Lab Assistant
Hatty Lee (Scott)
Research Technician
Joon Lee (Seung Kim)
Research Assistant
Harley McAdams
Senior Scientist
Ljiljana Milenkovic (Scott)
Research Specialist
Michelle Mittman (Talbot)
Research Technician
Maria Nagy
Glassware Washer
Kirsten Nereng (Kingsley)
Research Technician
Ann Reisenauer (Shapiro)
Research Associate
Margarita Roberts
Glassware Washer
Kaye Suyama (Scott)
Research Assistant
Abagail Thacker (Kingsley)
Research Technician
Cricket Wood (Fuller)
Research Assistant
David Weaver
Storekeeper
The departmental administrative staff is located in room B300 of the Beckman Center.
Susan Alexander
Administrative Associate (Fuller; Seung Kim; Talbot)
Ann Mischissin
Director of Finance and Administration
Todd Galitz
Laboratory Services Manager
Diane Bush
Administrative Assistant (Scott, Co-Chairman)
Kathy Shaw
Research Secretary (Nusse, Chairman) & Barsh)
Luella Luttman
Administrative Associate (Kaiser, Shapiro)
Aida Malimban
Administrative Assistant (Crabtree)
Flora Freitas
Personnel Coordinator &
A.A. (Hogness; Kingsley; Villeneuve)
Linda Quinn
Administrative Assistant (Weissman)
Graduate students are required by the University to register for autumn, winter, spring and summer quarters each year until the degree is received. Registration is also required each quarter in which a Stanford financial award is received. Leaves of absence require approval before departure.
Axess Application: http://axess.stanford.edu (a sunet id and password are required)
Axess is a student information system available via the web. It is regularly available weekdays 8:00 a.m.to 11:59 p.m. and weekends 9:00 a.m. to 11:59 p.m. Using Axess, you will be able to complete the following tasks:
New students may use Axess at any time after receipt of the registration packet from the Registrar's Office. You will need a SUNet ID and password, and PIN to use Axess.
Phone Axess
A voice response version of Axess is also available to provide end of term grade information, as well as graduation status for students who have applied to graduate. The number for Phone Axess is 650-725-AXES (725-2937). The hours are the same as for Axess (weekdays 8:00 a.m.to 11:59 p.m. and weekends 9:00 a.m. to 11:59 p.m.) You will be prompted to enter your student ID number and and the last four digits of your social security number to use Phone Axess.
Once you have accepted the offer of admission, you will be able to enroll in classes each quarter that you are at Stanford. The Registrar's Office will assume you plan to continue to enroll in classes every quarter (except summer) unless you inform the Registrar's Office that you do not plan to enroll for a particular quarter. Different procedures apply for undergraduates and graduates to cancel term activation (see the next section). Once you graduate, Axess will not allow you to enroll in future quarters unless you have been accepted into another program.
Your study list is the list of courses you are taking in a given quarter. You are required to submit your student list officially each quarter via the Axess Courses/Grades function. Study lists are due by 11:59 p.m. on the Sunday after the second week of instruction; late fees are charged for submission thereafter. Refer to the back cover of the Time Schedule (a listing of all courses taught, their meeting times, and locations) for specific instructions on how to file your study list.
A personal identification number (PIN) is required for access to AXESS; students that did not receive a PIN assignment in the mail can obtain a PIN at the Information window at the Registrar's Office in Old Union.
Refer to the back cover of the Time Schedule (a listing of all courses taught, their meeting times, and locations) for specific instructions on how to file your study list.
The Time Schedule includes the university calendar and information on registration procedures, payment of fees and course listings. It is published prior to each quarter and is available in Room B300, Beckman Center, the Graduate Student Affairs Office, MSOB, Room 309, the Medical School Student Affairs Office (M-105) and at the University Registrar's Office in the Old Union.
PIN NUMBER
All members of the Stanford community are assigned a University ID number (it's the 8 digit number above the picture on your University ID card) and a 5-8 digit Personal Identification Number (PIN). This ID/PIN combination verifies your identity when you sign electronic forms or request certain computer services. Your ID number is not secret but your SUNet ID/password and PIN must remain confidential. You should receive your ID and PIN number in the mail once your file has been processed. If you have forgotten your PIN, bring a photo ID to the Registrar's Office during business hours or send an e-email to Registrar@leland.stanford.edu. For further information log on to stanfordyou.edu or contact Todd Galitz, Lab Manager in Beckman B-300.
Your Stanford University ID is a number assigned to your academic record and is required for any inquiries you make. The ID number is printed on your registration commitment letter, your Stanford University ID card, and all enrollment/grading-related documents distributed by the Registrar's Office. Your ID number is unique and considered directory information. The first step in obtaining your ID card is to check with your student services administrator to be sure that your personnel file has been set up, and that you have been assigned an ID number. Once you have your number, you need to bring some form of picture ID with you to the ID Card Office. The ID Card office is located on the first floor of Old Union (Room 141), and its hours of operation are M-F, 8am - 12pm, and 1pm-5pm.
After submitting a Registration Commitment, students may receive a University bill. Tuition credits are entered on this bill. Also entered are other University charges such as rent, student fees, late fees, loans, etc. Students receiving a fellowship paid through Stanford may elect to have these charges deducted from their stipend checks and automatically applied to their bill.
If your bill is incorrect or incomplete, it is your responsibility to ensure that the bill is corrected or to pay the correct amount by the payment deadline.
Doctoral students are eligible for TGR status when they have been admitted to candidacy, completed all required coursework, completed 10.5 full-tuition quarters of residency or 135 unit if unit based, and submitted the Doctoral Dissertation Reading Committee form.
Students registered in TGR status must enroll each quarter in a TGR course (#802 for doctoral programs) in their department, with their advisor as the instructor. Work on the thesis, dissertation, or other remaining requirements must be evaluated each quarter for academic progress and graded as follows: "N" indicating satisfactory progress, "N-" for unsatisfactory progress, and "P" for a final grade when all requirements have been completed. A hold is placed on the registration of a student who receives an "N-" grade for two consecutive quarters. Further registration is contingent on approval of an agreement for completing degree requirements by the adviser and the department.
Curriculum
Course requirements for the Graduate Program in Developmental Biology are as follows:
1) Research (DB 399; 3 rotations during the first year)
2) Frontiers in Biological Sciences (DB215; taken each of the first two quarters during the first year).
3) Advanced Genetics (Genetics 203/ DB 203)
4) Developmental Biology (DB 210)
5) An advanced molecular biology, biochemistry, or biophysics course. Possible courses that would fulfill this requirement are: Graduate Molecular Biology (Biochem 201), Biological Macromolecules (Structural Biology 241), Physical and Chemical Principles of Biochemistry (Biochem 214), Computational Molecular Biology (Biochem 218), Principles of Cell Physiology (MCP 210), Protein and Nucleic Acid Structure, Dynamics and Engineering (Structural Bio 228), Eukaryotic Chromosome (Structural Bio 229). Other courses not listed may be used to fulfill this requirement contingent on prior approval of the Graduate Student Coordinator. Alternatively, this requirement may be fulfilled by acting as a T.A. for Biochemistry 200 or 203.
6) At least two additional courses.
Letter grades will be given for all core courses except Frontiers. Students are also expected to attend regular Developmental Biology seminars and journal clubs. In addition to the required courses, many students also take Cell Biology of Physiological Processes (MCP211; offered in the Winter quarter), and may choose from a variety of elective courses that are offered on a rotating basis. The first year students should meet with their Advisory Committees to determine their course schedules. Course requirements are usually fulfilled during the first two years of study and the latter years of the program are devoted to full-time research and work on the dissertation. The University requires that a minimum of three (3) units of coursework be taken with each of four (4) or more Stanford faculty members, not necessarily within the major department.
In this Seminar we will investigate recent pioneering research into the molecular and genetic mechanisms that guide normal development of the mammalian brain. We will look at initial events that create neural cells, how distinct functional domains are formed in the brain, and how the initial "wiring" of the brain during development is accomplished. We will see how studies of brain development using a variety of animals are informative about our own brain development. We will look at molecules that control brain development from an evolutionary perspective and from a systems design perspective. We will discuss medical consequences of malfunctions in those mechanisms, and the implications of recent research for regeneration and therapy.
3 units, Spr (Scott)
This course will focus on the underlying genetic logic used to dissect apart diverse biological phenomena. The course explores the genetic toolbox through studies of analytic methods and modern synthetic genetic manipulation, including original papers. Emphasis is on use of genetic tools in dissecting complex biological pathways, developmental processes, and regulatory systems. We will discuss classical genetic approaches as well as newer approaches being developed in the post-genome era (in which the entire genomic sequence of an organism is known.) Graduate students in any one of the biological sciences are welcome, but those with minimal experience in genetics should prepare themselves by working through problems in Hartl, et al and Jones.
4 units, Aut (D. Botstein, Stuart Kim, T. Stearns, A. Villeneuve)
(Same as Biological Sciences 204 and Genetics 204). Continues exploration, begun in Genetics 203, of basic concepts and experimental design in modern Genetics. Emphasis is placed on studying genetic systems in detail from original papers as well as the impact of genomics on experimental design and practice. Prerequisite: Genetics 203.
3 units, Win (D. Bostein, A. Villeneuve, Stuart Kim, and T. Stearns) offered upon request of students
This course focuses on the mechanisms that direct human development, from conception to birth. Conserved molecular and cellular pathways regulate tissue and organ development in humans and other species. Errors in these pathways result in congenital anomalies, and common human diseases. Topics include: molecules regulating development, cell induction, developmental gene regulation, cell migration, programmed cell death, pattern formation, stem cells, cell lineage, and development of major organ systems. Emphasis is devoted to links between development and clinically significant topics, including infertility, assisted reproductive technologies, contraception, pre-natal diagnosis, multiparity, teratogenesis, inherited birth defects, and fetal therapy. Lectures connect fundamental discoveries in developmental biology to advances in disease diagnosis, therapy, and prevention in clinical medicine.
2 units, Autumn (M. Scott, E. Porzig, D. Kingsley, and Seung Kim)
The goal of the course is to discover unifying themes in how organismic complexity is generated during embryonic and post-embryonic development. The roles of genetic hierarchies, induction events, cell lineage, maternal inheritance, cell-cell communication and hormonal control in developmental processes in well-studied organisms such as mammals, zebrafish, insects and nematodes will be discussed. This course is designed to acquaint graduate students and advanced undergraduates (with permission of the instructor only) with important current areas of research in developmental biology. It is recommended that preparation for the course include familiarity with basic techniques and experimental rationales of molecular biology, biochemistry and genetics. Two lectures each week will be accompanied by a third meeting during which small groups of students will meet with faculty to discuss current papers from the literature in depth. Team taught by members of the faculty of Developmental Biology.
5 units, Spr (Talbot, Fuller, Crabtree, Kingsley, Nusse, Scott, Seung Kim)
Faculty-student discussion course with emphasis on how to critically evaluate primary research literature in many different areas of biological research. Held in conjunction with a Wednesday seminar series, hosted in alternate weeks by the departments of Biochemistry, Genetics, Developmental Biology. Each Wednesday a distinguished investigator will present their current work at the frontiers of biological research. Before the seminar, students and course faculty will meet and discuss in depth one or more papers from the primary research literature on a related topic. After the Wednesday seminar, students will have the opportunity to meet informally with the seminar speaker to discuss their research and future directions. Emphasis is on how to read papers in the primary research literature, the set of techniques most commonly used to study problems in biology and a comparison between genetic and biochemical approaches in biological research.
1 unit, Aut, Win (D. Kingsley, P. Harbury, Stuart Kim)
Topics: imprinting, early development and implantation, germ cell allotment, phenotypic consequences of targeted knockouts of developmental genes, hox genes and other developmental genes in mammals, tumorigenesis, coat color mutations, classical mutations and positional cloning, mutagenesis and insertional and gene traps, growth controls, muscle and limb development, sex determination, classical genetics and gene mapping and inbred strains, segregation and T locus, and germ and embryonic stem cells and teratocarcinomas. One lecture per week, plus either one guest lecture or a literature discussion.
2 units, Win (Barsh, Nusse) offered every two years, not offered 2000-01
The molecular basis of energy transduction that leads to movements generated by microfilament-based and microtubule-based motors. In depth analysis of forms of myosin, dynein, and kinesin and their roles in the cell, as a model for understanding the structural, biochemical, and functional properties of biological machines in general. Topics: structure of the molecular motors and their accessory proteins: regulation of the function of motile assemblies; functions of molecular motors in cells. Experimental approaches: genetic analysis, DNA cloning and expression, reconstitution of functional assemblies from purified proteins, x-ray diffraction, three-dimensional reconstitution of electron microscope images, spectroscopic methods, and high-resolution light microscopy. Focuses on how a complex cellular process is analyzed at the molecular level by a multifaceted approach using biomedical, biophysical, and genetic techniques. Prerequisites: knowledge of basic biochemistry and cell biology.
3 units, Aut (M. Fuller, J. Spudich) not offered 2000-01
(Same as Biochemistry 237, Biological Sciences 237, Biophysics 237, Chemistry 237, Civil Engineering 237, Developmental Biology 237, and Structural Biology 237). Faculty from the Departments of Biochemistry, Biological Sciences, Chemical Engineering, Chemistry, Civil Engineering, Civil Sciences, Developmental Biology, and Structural Biology and invited industrial speakers review the interrelated elements of modern biotechnology. Topics: protein structure and dynamics, protein engineering, biocatalysis, gene expression, cellular metabolism and metabolic engineering, fermentation technology, and purification of biomolecules. Prerequisite: graduate student or upper-division undergraduate in the sciences and engineering.
3 units, Spr (C. Robertson)
Prerequisite(s): consent of instructor. See faculty list for section numbers.
1 to 18 units, any quarter, by arrangement
Allows for qualified students to undertake investigations sponsored by individual faculty members. Prerequisite(s): consent of instructor. See faculty list for section numbers.
1 to 18 units, any quarter, by arrangement.
Biosciences --(Cross-listed in multiple departments in the schools of Humanities and Sciences, Engineering, and Medicine; students should enroll directly through their affiliated department, if at all possible.) Introduction to cutting-edge research involving interdisciplinary approaches to bioscience and biotechnology; for specialists and non-specialists. Associated with Stanford's Clark Center for Interdisciplinary Bioscience, and held in conjunction with a seminar series meeting twice monthly during 2000-01. Leading investigators from Stanford and throughout the world speak on their research; students also meet separately to present and discuss the ever-changing subject matter, related literature, and future directions. Prerequisite: keen interest in all of science, with particular interest in life itself. Recommended: basic knowledge of biology, chemistry, and physics.
2 units (S. Block)
Research rotations are an important part of the graduate training program. The purpose of laboratory rotations is to broaden the student's research experience and to familiarize students with the ongoing research projects in a variety of different laboratories. While a primary function of rotations is to help students choose a Ph.D. advisor, students should also use the rotations to learn as much as possible about research in developmental biology at Stanford.
First-year students spend one quarter in each of three different labs, working closely with the professor, graduate students and postdoctoral fellows on research projects. The Fall quarter rotation must be in a laboratory within the Department of Developmental Biology. Rotations during the Winter and Spring quarters may be in any laboratory within the Biosciences at Stanford. It is the student's responsibility to contact appropriate faculty members to arrange lab rotations. During the fourth quarter, the student chooses a permanent laboratory in which to carry out his/her dissertation research.
There is no formal teaching requirement in the Department of Developmental Biology. Students interested in gaining teaching experience may serve as teaching assistants in several courses, with approval of the course instructors and after consultation with the Advisory Committee.
Upon entering the department in the fall of the first year, the new student is assigned an Advisory Committee of three faculty members. This committee will include the student's first rotation advisor and the First Year Student Coordinator (William Talbot). The Committee is responsible for advising students on courses to take, choices for laboratory rotations, and other issues that may arise during the first year.
The Departments of Developmental Biology and Biochemistry each sponsors a biweekly departmental seminar series held on alternating Wednesday afternoons. The "Frontiers in Developmental Biology" and "Frontiers in Biochemistry" seminar series bring outstanding developmental biologists and biochemists, both nationally and internationally recognized, to Stanford to present their work. To recognize and promote participation by the students, the departments jointly offer one unit of credit for a seminar course, "Frontiers in Biological Research" associated with these seminar series. In this course, students will read and discuss literature related to the topic being presented. Students have the opportunity to meet with each speaker after the seminar for an informal discussion.
The Frontiers in Developmental Biology seminars take place at 4 pm in room M106 in the Medical Center. Coffee and cookies are served at 3:30 pm. A reception with the speaker follows in the Developmental Biology library (Room B302) after the seminar. The dates and speakers for the 2000-01 series to be announced:
An important aspect of the training of every graduate student is the development of speaking skills. The department provides numerous opportunities for trainees to speak about their research in a seminar setting. Once students begin their dissertation work in the second year, they will be asked to give a talk in the department about once a year. Student talks can be given in one of the many research interest groups, such as the Microbial Data or "Dev Bio Departmental Data Club ("3D") or RAVE, or at the departmental conference. This is a valuable experience because all members of the department, including faculty attend the seminars. These seminars will be concerned with ongoing and unfinished work and consequently are expected to generate considerable discussion. The speaker must organize the work, present it clearly, answer questions, and discuss other ideas raised by the listeners.
3D, Discussing Developmental Data: 3D is an informal research meeting at which graduate students and postdocs present their latest results and ideas to the entire department. These lunch-time discussions are lively and informative, reflecting the enthusiasm and cutting-edge research of graduate students, postdoctoral fellows, and faculty of the Department.
Most students participate in journal clubs that meets on a regular schedule to discuss published reports from the literature. The goal of these Journal Clubs is to teach students to read, analyze and criticize scientific papers. Students are exposed to a broad sampling of research interests and experimental approaches. All students participate actively in critiquing the papers, and each student is given the responsibility for leading discussions several times throughout the year.
The Microbial Data Club is an informal gathering of approximately 50 graduate students, postdocs and faculty who have a research interest in prokaryotic and eukaryotic microbes. The "Bug Club" meets the second Thursday of every month from 6-8 pm in the Developmental Biology library. Dinner can be purchased inexpensively for the first half-hour. Two talks of about 20-30 minutes are presented and there is plenty of time for questions. In the past year, participants from the following departments have taken part: Biological Sciences, Biochemistry, Developmental Biology, Genetics, and Microbiology and Immunology.
Research About Vertebrate Embryos (RAVE): Every month Bay Area labs working on vertebrate development meet to discuss ongoing research projects utilizing fish, frogs, chicks, mice, and humans. Two half-hour research talks are usually presented, with lots of time for questions and discussion. Meetings alternate between Stanford, Berkeley, and UCSF.
Pizza and soft drinks provided. Meeting times and topics posted near B307 and on departmental bulletin boards. Contact the Kingsley laboratory for more information.
Each faculty member in the department schedules weekly group meetings in which the students and postdoctoral fellows take turns presenting their experiments and/or discussing papers from the literature.
Every 2-3 years, students and postdocs organize a two-day symposium focused on a particular topic in Developmental Biology. Expert scientists in the field are brought together to probe the subject in depth. The Symposium will be held on April 17-18. Previous symposia topics include: "Cell Migration During Development", and "Evolution of Genetic and Developmental Programs". And "Cellular Asymmetry".
Two long-standing DB traditions are snacks provided by the department at 4:30 p.m. on Mondays and on Wednesdays when there is no seminar, and a Social Hour held Friday afternoons at 5:30 p.m. (sponsored by different lab groups on a rotating basis). Both gatherings are held in the 3rd Floor lobby.
The purpose of the qualifying examination is to give students the opportunity to demonstrate that they can formulate a research project, devise a strategy for testing hypotheses, utilize appropriate methods, critically interpret results, and present their ideas clearly and succinctly. The exam consists of two proposals, each written in the form of a scientific grant proposal. The preparation and defense of a research proposal is a useful indicator of a student's capabilities and provides valuable training in the important skill of preparing grant proposals to support research efforts.
One of the two proposals is on a subject different from the dissertation research and different from previous work submitted for a course. The other is on the planned subject of the thesis. The graduate student decides the order of the two proposals. The first proposal must be prepared and defended during January of the second academic year. The second proposal must be prepared and defended during November of the third academic year. This will allow both proposals to be prepared and defended satisfactorily in time to declare Ph.D. candidacy by Winter quarter of the third year.
The qualifying exam committee will consist of the student's thesis advisor, the chairperson for the qualifying exams and two additional faculty members. The chairperson will be the same for all students in a class. The student will choose the two additional faculty on the committee after consulting with the chairperson and the student's thesis advisor. If the chair is also the student's thesis advisor, another faculty member will be chosen by the student to serve on the committee. The examination committee will provide general advice during the preparation of the proposal.
The research proposals should be approached as a 3-year, one-person project (similar to the basis of a postdoctoral fellowship application). A short presentation before the examination committee may be requested. Visual aids (e.g., slides or overheads) are acceptable. Below are more detailed instructions on writing the proposals:
Research Plan. Organize Sections A-D of the Research Plan to answer these questions. (A) What do you intend to do? (B) Why is the work important? (C) What has already been done? (D) How are you going to do the work? Do not exceed 20 double-spaced pages for Sections A-D. You may use any page distribution within this overall limitation; however, the advisory committee recommends the following format and distribution:
A. Specific Aims. State the broad, long-term objectives and describe concisely and realistically what the specific research described in this application is intended to accomplish and any hypotheses to be tested. One page is recommended.
B. Background and Significance. Briefly sketch the background to the present proposal, critically evaluate existing knowledge, and specifically identify the gaps that the project is intended to fill. State concisely the importance of the research described in this application by relating the specific aims to the broad, long-term objectives. Two to three pages are recommended.
C. Progress Report (second proposal only). A progress report is required for proposed thesis research. Use this section to provide an account of preliminary studies pertinent to the proposal. Six to eight pages are recommended. For the first proposal that does not have a progress report, use the additional pages for Section D.
D. Experimental Design and Methods. Outline the experimental design and the procedures to be used to accomplish the specific aims of the project. Include the means by which the data will be collected, analyzed, and interpreted. Describe any new methodology and its advantage over existing methodologies. Discuss the potential difficulties and limitations of the proposed procedures and alternative approaches to achieve the aims. Although no specific number of pages is recommended for this section, the total for Sections A-D may not exceed 20 double-spaced pages.
After the presentation, the committee will ask questions broadly related to the proposal. The student is expected to understand and be able to clearly explain relevant biochemistry and genetics principles and procedures. In addition, the student may be asked to justify the particular approaches presented in each proposal. A working knowledge of the scientific literature relevant to the planned experiments will be expected. The questions may cover related material from previous courses or from laboratory rotations. The examination results in a Pass or a Fail. If a student fails, he or she may be allowed to remedy deficiencies. This could include any of the following: rewriting of the proposal, a second examination on the same topic or on another topic, the presentation of a seminar, or the successful completion of additional coursework. The Committee on Graduate Studies will recommend the student for admission to candidacy only after successfully passing the qualifying examination.
The Ph.D. thesis and oral examination are expected to be finished within five and one-half years from the date of entrance into the graduate program. The following process is designed to facilitate this expectation and to promote faculty participation.
The dissertation committee will consist of four faculty members. These will include the student's thesis advisor, another departmental faculty member who will serve as chair, and two other faculty members who can come from either inside or outside the department. The student subject to prior departmental approval will choose committee members from outside the department.
The dissertation committee will initially be the same as the committee for the qualifying exam, but can be changed by the student, subject to prior departmental approval, to best reflect the research interests of the student. The dissertation committee will follow the student's progress from completion of the qualifying examination to the dissertation defense. The membership for the dissertation committee should not be changed after the penultimate meeting, scheduled approximately six months before the expected date of completion of the dissertation.
By the end of the last quarter of year three, the student in consultation with the research advisor should present to the student's dissertation committee for its review and acceptance a plan and timetable for finishing the Ph.D. During the third quarter of years four and five, the student should similarly meet with the dissertation committee to report on her/his progress. For each of these meetings, the student should prepare an outline of the research plan to hand out to the committee members in advance. In a minority of cases, completion of the Ph.D. by the end of the second quarter of year six may not be anticipated at either of these committee meetings. In these cases, the student in consultation with the research advisor should present to the committee for their approval a revised plan for completion. This plan is to include meetings with the student's committee every other quarter and the expected sources of stipend support after the second quarter of year six. Should the source of this stipend support not be obvious, the student in consultation with the research advisor will submit to the committee a written request to the Department for that support.
When the student, advisor, and Dissertation Committee agree that the student has completed work of sufficient novelty and quality to merit the Ph.D., the student will write a dissertation. When the dissertation is acceptable to the advisor, it will be presented to the Dissertation Defense Committee. The student will then defend this dissertation at the University oral examination.
University regulations specify the composition of the examination committee and the format of the dissertation defense. The department requires that the student present a formal seminar to the members of the department. The formal seminar is held immediately prior (on the same day) to the dissertation defense. The dissertation is expected to be an original contribution to scholarship, to exemplify the highest standards of the discipline, and to be of lasting value to the intellectual community. University guidelines for presentation of doctoral work are described in Directions for Preparing Doctoral Dissertations. These guidelines should be read carefully before final preparation of the manuscript to avoid costly and time-consuming revisions.
Published papers may be included in dissertations; however, they must meet the University's format guidelines. Manuscripts and figures submitted for publication during the doctoral program should be retained for later reformatting and inclusion in the dissertation. Dissertations must be in English.
The Doctoral Dissertation Reading Committee approves the dissertation. Each member of the dissertation committee signs the signature page of the dissertation to certify that the work is of acceptable scope and quality. One reading committee member reads the dissertation in its final form and certifies that departmental and University specifications have been met.
Deadlines for submission of dissertations are strictly enforced. Students who submit their dissertations after the deadline in a given quarter may obtain a Statement of Completion from the Graduate Degree Support Section; official conferral will occur in the following quarter.
The Doctoral Dissertation Reading Committee consists of the principal dissertation adviser and two other readers. At least one member must be from the major department. At least two members must be on the Academic Council. (Approval for appointment of a reader who is not on the Academic Council may be given by the Graduate Degree Support Section if that person is particularly well qualified to consult on the dissertation topic.).
The reading committee is endorsed by the chair of the major department on the Doctoral Dissertation Reading Committee form. This form is submitted to the Graduate Degree Support Section before approval of Terminal Graduate Registration (TGR) status or before scheduling a University oral examination that is a defense of the dissertation, whichever comes first in the program.
A University oral examination is a requirement of the Ph.D. program. The purpose of the examination is to test the candidate's command of the field of study and to confirm fitness for scholarly pursuits. The University oral examination will be administered according to the following guidelines:
1. The chair must be an Academic Council member from a department not represented by members of the examining committee.
2. At least four examiners are required, three of which must be on the Academic Council. A fourth member who is not on the Academic Council may be substituted if he or she contributes an area of expertise not readily available from the faculty and if approved upon petition to the Graduate Degree Support Section.
3. The student's candidacy must be valid and registration is required in the quarter in which the oral examination is taken. The Doctoral Dissertation Reading Committee form must be on file in the Graduate Degree Support Section before oral examinations that are a dissertation proposal or defense.
4. The student's department delivers to the chair a University oral examination schedule, University Guidelines for Oral Examination Procedures, and an abstract for oral examinations that are a dissertation proposal or defense.
5. The oral examination results are validated by the chair and reported to the department and the Graduate Degree Support Section within five days of the examination.
6. University procedures are followed in communicating with students who do not pass the examination. Copies of this correspondence will continue to be sent to the Graduate Degree Support Section.
Oral examinations should be scheduled at least ten days before the examination date to allow sufficient time to send announcements to the Stanford Report.
The Notice of Intention to Complete Advanced Degree Requirements form is submitted to the Graduate Degree Support Section to initiate approval for conferral of all graduate degrees. It should be submitted preferably in the second week, but no later than the last day of classes of the degree quarter, as listed in the University Calendar. Requests for conferral are reviewed by the Graduate Degree Support Section and the department to verify completion of degree requirements. In Summer, Autumn, and Winter Quarters degree certificates are sent to students within two weeks of the conferral date.
The Graduate Degree Support Section should be notified in writing when conferral plans change. Students who withdraw their conferral request or who fail to complete degree requirements must file a new Notice of Intention for a subsequent quarter. A new Notice of Intention must be filed for each degree and conferral quarter.
Commencement ceremonies are held each June for students who have received degrees in the previous Summer, Autumn, Winter and Spring quarters. Students who wish to receive their diplomas at June commencement must submit a Notice of Intention by February 1 to allow adequate time for preparation of the diploma. Information on Commencement activities and distribution of diplomas is sent by the Registrar's Office in early April to addresses provided on the Notice of Intention. Students who wish to participate in commencement activities in advance of conferral of their degree may obtain a Graduate Student Petition to Walk Through Commencement Exercises from the Graduate Program Office from May 1 until the day before commencement. A Walk Through petition should be requested only if there is no possibility of completing degree requirements for June conferral.
Entering students are normally offered research assistantships, fellowships, or traineeships that include payment of a stipend and tuition. Students are strongly encouraged to apply for predoctoral fellowships from the National Science and Howard Hughes Foundations by November of their first year in residence. Applications for both are available in October and due in November. Check with the Graduate Support Section of Financial Aid for further details. Students are also encouraged to apply for other outside fellowships. The Awards Data Base available on Folio (a computer on-line system) contains information on over 1,200 awards of academic interest. Departmental funds are used to supplement support from all sources to an annual level of $21,000 for 2000-01 and to pay for health insurance. Student fees, late fees, etc. are the responsibility of each student. Students may receive stipends quarterly or semi-monthly.
For those students on fellowships who are paid quarterly, the stipend checks are issued the day before classes begin. Checks are sent to the department and students are required to sign for them.
Students who are paid semi-monthly will be paid on the 7th and the 22nd of the month (or on the preceding work day if these dates fall on a weekend or holiday). Checks are sent to the department.
Semi-monthly paychecks may be directly deposited in local banks upon request to the departmental business office staff.
M.D./Ph.D. students can pick up check in the Developmental Biology Administrative Office, B-300
Outside employment is discouraged.
Stanford University's health and safety mission is to provide a safe and healthy environment for faculty, students and staff and to assure compliance with federal, state and local regulations. The University Environmental Health and Safety (EH&S) office manages health and safety programs for the Medical School such as:
Each person working in a lab is required to be trained in the specific hazards of his or her job. Laboratory safety is a component of the orientation to a research lab. It is the Principal Investigator's responsibility to provide training for lab equipment, procedures and chemicals. EH&S provides two mandatory training sessions.
EH&S, through the Health Physics Department, provides mandatory training for use of radioisotopes as part of Stanford's licensing agreement with the State of California. New students need to contact Health Physics and complete the following before they can work with any radioactive material:
In conjunction with the Medical School's Health and Safety Program office, EH&S provides mandatory Lab Safety Training. The office also assists in resolving safety problems and provides each department Safety Team with safety information and regulatory compliance strategies. EH&S provides a variety of environmental health and safety services:
The on-line Chemical Safety Database
Emergency Response Team available 24 hours a day
Hazardous waste pick up
Safety related reference material (books and videos)
The department has developed a Health and Safety Team made up of representatives of the research and administrative staffs and students. The principal investigator on the team is Dale Kaiser. Their initial goals will focus on compliance issues, education and training, disaster preparedness and accident reporting. They also maintain copies of the Radiation Safety Manual, Stanford Biohazardous Materials Guidelines, Stanford Safety Manual and Material Safety Data Sheets (MSDS) and department training records.